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<!DOCTYPE html><html lang=en> <head><link rel=stylesheet type=text/css href="https://fonts.googleapis.com/css?family=Overpass:300,400,600,800"><script src=https://code.jquery.com/jquery-3.4.1.min.js integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin=anonymous></script><link href=https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css rel=stylesheet integrity=sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T crossorigin=anonymous><script src=https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js integrity=sha384-JjSmVgyd0p3pXB1rRibZUAYoIIy6OrQ6VrjIEaFf/nJGzIxFDsf4x0xIM+B07jRM crossorigin=anonymous></script><link rel=stylesheet type=text/css href="doc_assets/schema_doc.css"><script src=https://use.fontawesome.com/facf9fa52c.js></script><script src="doc_assets/schema_doc.min.js"></script><meta charset=utf-8><title>V-pipe configuration</title></head> <body onload=anchorOnLoad(); id=root><h1>V-pipe configuration</h1><div class=text-right> <button class="btn btn-primary" type=button data-toggle=collapse data-target=.collapse:not(.show) aria-expanded=false>Expand all</button> <button class="btn btn-primary" type=button data-toggle=collapse data-target=.collapse.show aria-expanded=false>Collapse all</button> </div> <div class=breadcrumbs></div><span class="badge badge-dark value-type">Type: object</span><br> <span class=description><p>The V-pipe workflow can be customized through the configuration file <code>config.yaml</code> or <code>config.json</code> or, for backward compatibility with the <a href=https://github.com/cbg-ethz/V-pipe/wiki/options>legacy INI-style format used in V-pipe v1.x/2.x</a>, <code>vpipe.config</code>. This configuration file is a text file written using a basic structure composed of sections, properties and values. When using <a href=https://yaml.org/spec/1.0/#id2564813>YAML</a> or <a href=https://www.json.org/json-en.html>JSON</a> format use these languages associative array/dictionaries in two levels for sections and properties. When using the older <a href=https://docs.python.org/3/library/configparser.html>INI format</a>, sections are expected in squared brackets, and properties are followed by corresponding values.</p> <p>Further more, it is possible to specify additional options on the command line using Snakemake’s <code>--configfile</code> to pass additional YAML/JSON configuration files, and/or using Snakemake’s <code>--config</code> to pass sections and properties in a <a href=https://yaml.org/spec/1.2.0/#Flow>YAML Flow style</a>/JSON syntax.</p> <p>The order of precedence is:<br> <em>command line options (<code>--config</code>, <code>--configfile</code>)</em> >> <em>default configuration file (<code>config/config.yaml</code> or <code>config.yaml</code>)</em> >> <em>legacy configuration INI (<code>vpipe.config</code>)</em> >> <em>Virus-specific base config (<code>virus_based_config</code>)</em> >> <em>default values</em></p> <p>Example: For instance, we suggest providing as input a tabular file specifying sample unique identifiers (e.g., patient identifiers), and dates for different sequencing runs related to the same patient. The name of this file (here, <code>samples.tsv</code>) can be provided by specifying the section as <code>input</code> and the property as <code>samples_file</code>, as follows in the example below.</p> <p>In this document, we provide a comprehensive list of all user-configurable options stratified by sections.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=root_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class=nt>input</span><span class=p>:</span><span class=w></span>
<span class=w> </span><span class=nt>samples_file</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">samples.tsv</span><span class=w></span>
</pre></div> </div> <div class=accordion id=accordiongeneral> <div class=card> <div class=card-header id=headinggeneral> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#general aria-expanded aria-controls=general onclick="setAnchor('#general')"><span class=property-name>general</span></button> </h2> </div> <div id=general class="collapse property-definition-div" aria-labelledby=headinggeneral data-parent=#accordiongeneral> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general onclick="anchorLink('general')">general</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <span class=description><p>This section of the configuration provides general options that control the overall behavior of the pipeline.</p> </span> <div class=accordion id=accordiongeneral_virus_base_config> <div class=card> <div class=card-header id=headinggeneral_virus_base_config> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#general_virus_base_config aria-expanded aria-controls=general_virus_base_config onclick="setAnchor('#general_virus_base_config')"><span class=property-name>virus_base_config</span></button> </h2> </div> <div id=general_virus_base_config class="collapse property-definition-div" aria-labelledby=headinggeneral_virus_base_config data-parent=#accordiongeneral_virus_base_config> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general onclick="anchorLink('general')">general</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general_virus_base_config onclick="anchorLink('general_virus_base_config')">virus_base_config</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>We provide virus-specific base configuration files which contain handy defaults for, e.g., HIV and SARS-CoV-2. Check the git repository’s <a href=https://github.com/cbg-ethz/V-pipe/tree/master/config#virus_base_config>config subdirectory</a> to learn about them.</p> </span> <br> <div class="badge badge-secondary">Examples:</div> <br><div id=general_virus_base_config_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">hiv</span><span class=w></span>
</pre></div> </div><div id=general_virus_base_config_ex2 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">sars-cov-2</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiongeneral_preprocessor> <div class=card> <div class=card-header id=headinggeneral_preprocessor> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#general_preprocessor aria-expanded aria-controls=general_preprocessor onclick="setAnchor('#general_preprocessor')"><span class=property-name>preprocessor</span></button> </h2> </div> <div id=general_preprocessor class="collapse property-definition-div" aria-labelledby=headinggeneral_preprocessor data-parent=#accordiongeneral_preprocessor> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general onclick="anchorLink('general')">general</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general_preprocessor onclick="anchorLink('general_preprocessor')">preprocessor</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "prinseq"</span><br> <span class=description><p>By default trimming and clipping of reads is performed by PRINSEQ <sup class=footnote-ref id=fnref-10><a href=#fn-10>1</a></sup> – a versatile raw read processor for short-reads with many customization options, that we use mostly for Illumina short-read sequencing.<br> Some other sequencing platforms, e.g., Oxford Nanopore Technologies, are not compatible with this software and usually perform quality control during the fast5 basecalling and demultiplexing anyway, e.g., by Guppy. Use <code>skip</code> to avoid performing preprocessing such already quality-trimmed fastq files.</p> <div class=footnotes> <hr> <ol> <li id=fn-10> <p>Schmieder, R. and Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011. <a href=#fnref-10 class=footnoteBackLink title="Jump back to footnote 1 in the text.">↩</a></p> </li> </ol> </div> </span><div class=enum-value id=general_preprocessor_enum> <h4>Must be one of:</h4> <ul class=list-group><li class="list-group-item enum-item">"prinseq"</li><li class="list-group-item enum-item">"skip"</li><li class="list-group-item enum-item">""</li></ul> </div> <br> <div class="badge badge-secondary">Example:</div> <br><div id=general_preprocessor_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">skip</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiongeneral_aligner> <div class=card> <div class=card-header id=headinggeneral_aligner> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#general_aligner aria-expanded aria-controls=general_aligner onclick="setAnchor('#general_aligner')"><span class=property-name>aligner</span></button> </h2> </div> <div id=general_aligner class="collapse property-definition-div" aria-labelledby=headinggeneral_aligner data-parent=#accordiongeneral_aligner> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general onclick="anchorLink('general')">general</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general_aligner onclick="anchorLink('general_aligner')">aligner</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "ngshmmalign"</span><br> <span class=description><p>There are three options for mapping reads, either using <a href=https://github.com/cbg-ethz/ngshmmalign><code>ngshmmalign</code></a>, <a href=https://github.com/lh3/bwa>BWA MEM (<code>bwa</code>)</a> <sup class=footnote-ref id=fnref-1><a href=#fn-1>1</a></sup>, <a href=http://bowtie-bio.sourceforge.net/bowtie2/index.shtml>Bowtie 2 (<code>bowtie</code>)</a> <sup class=footnote-ref id=fnref-2><a href=#fn-2>2</a></sup>, or <a href=https://lh3.github.io/minimap2/ >minimap2 (<code>minimap</code>)</a><sup class=footnote-ref id=fnref-11><a href=#fn-11>3</a></sup>. To use a different aligner than the default, indicate which aligner you want to use by setting the property aligner.</p> <p><strong>Note</strong>: Some virus-specific base configuration specified in <code>virus_base_config</code> might change this option’s default to a more appropriate aligner for that virus, e.g., depending on its usual diversity and mutation rate.<br> You are still free to override that default in your configuration shall the need arise.</p> <div class=footnotes> <hr> <ol> <li id=fn-1> <p>Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013. <a href=#fnref-1 class=footnoteBackLink title="Jump back to footnote 1 in the text.">↩</a></p> </li> <li id=fn-2> <p>Langmead, B. and Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012. <a href=#fnref-2 class=footnoteBackLink title="Jump back to footnote 2 in the text.">↩</a></p> </li> <li id=fn-11> <p>Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018. <a href=#fnref-11 class=footnoteBackLink title="Jump back to footnote 3 in the text.">↩</a></p> </li> </ol> </div> </span><div class=enum-value id=general_aligner_enum> <h4>Must be one of:</h4> <ul class=list-group><li class="list-group-item enum-item">"ngshmmalign"</li><li class="list-group-item enum-item">"bwa"</li><li class="list-group-item enum-item">"bowtie"</li><li class="list-group-item enum-item">"minimap"</li></ul> </div> <br> <div class="badge badge-secondary">Example:</div> <br><div id=general_aligner_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">minimap</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiongeneral_primers_trimmer> <div class=card> <div class=card-header id=headinggeneral_primers_trimmer> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#general_primers_trimmer aria-expanded aria-controls=general_primers_trimmer onclick="setAnchor('#general_primers_trimmer')"><span class=property-name>primers_trimmer</span></button> </h2> </div> <div id=general_primers_trimmer class="collapse property-definition-div" aria-labelledby=headinggeneral_primers_trimmer data-parent=#accordiongeneral_primers_trimmer> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general onclick="anchorLink('general')">general</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general_primers_trimmer onclick="anchorLink('general_primers_trimmer')">primers_trimmer</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "ivar"</span><br> <span class=description><p>There are two options available for trimming primers, either using <a href=https://andersen-lab.github.io/ivar/html/ >iVar trim (<code>ivar</code>)</a> <sup class=footnote-ref id=fnref-3><a href=#fn-3>1</a></sup> or <a href=http://www.htslib.org/doc/samtools-ampliconclip.html>Samtools ampliconclip (<code>samtools</code>)</a> <sup class=footnote-ref id=fnref-4><a href=#fn-4>2</a></sup>. iVar trim is used by default. If you prefer to use Samtools ampliconclip, then indicate so in the configuration file as in the example</p> <div class=footnotes> <hr> <ol> <li id=fn-3> <p>Grubaugh, N. et al. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biology. 2019. <a href=#fnref-3 class=footnoteBackLink title="Jump back to footnote 1 in the text.">↩</a></p> </li> <li id=fn-4> <p>Danecek P, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021 <a href=#fnref-4 class=footnoteBackLink title="Jump back to footnote 2 in the text.">↩</a></p> </li> </ol> </div> </span><div class=enum-value id=general_primers_trimmer_enum> <h4>Must be one of:</h4> <ul class=list-group><li class="list-group-item enum-item">"ivar"</li><li class="list-group-item enum-item">"samtools"</li></ul> </div> <br> <div class="badge badge-secondary">Example:</div> <br><div id=general_primers_trimmer_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">samtools</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiongeneral_snv_caller> <div class=card> <div class=card-header id=headinggeneral_snv_caller> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#general_snv_caller aria-expanded aria-controls=general_snv_caller onclick="setAnchor('#general_snv_caller')"><span class=property-name>snv_caller</span></button> </h2> </div> <div id=general_snv_caller class="collapse property-definition-div" aria-labelledby=headinggeneral_snv_caller data-parent=#accordiongeneral_snv_caller> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general onclick="anchorLink('general')">general</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general_snv_caller onclick="anchorLink('general_snv_caller')">snv_caller</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "shorah"</span><br> <span class=description><p>There are three options available for calling single nucleotide variants, either using <a href=https://github.com/cbg-ethz/shorah>ShoRAH (<code>shorah</code>)</a> <sup class=footnote-ref id=fnref-5><a href=#fn-5>1</a></sup>, <a href=https://csb5.github.io/lofreq/ >LoFreq (<code>lofreq</code>)</a> <sup class=footnote-ref id=fnref-6><a href=#fn-6>2</a></sup> or <a href=https://github.com/cbg-ethz/viloca>VILOCA (<code>viloca</code>)</a> [^7] . ShoRAH is used by default. If you prefer to use LoFreq, then indicate so in the configuration file as in the example</p> <div class=footnotes> <hr> <ol> <li id=fn-5> <p>Zagordi, O. et al. ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinformatics. 2011. <a href=#fnref-5 class=footnoteBackLink title="Jump back to footnote 1 in the text.">↩</a></p> </li> <li id=fn-6> <p>Wilm, A. et al. LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 2012. <a href=#fnref-6 class=footnoteBackLink title="Jump back to footnote 2 in the text.">↩</a></p> </li> </ol> </div> </span><div class=enum-value id=general_snv_caller_enum> <h4>Must be one of:</h4> <ul class=list-group><li class="list-group-item enum-item">"shorah"</li><li class="list-group-item enum-item">"lofreq"</li><li class="list-group-item enum-item">"viloca"</li></ul> </div> <br> <div class="badge badge-secondary">Example:</div> <br><div id=general_snv_caller_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">lofreq</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiongeneral_haplotype_reconstruction> <div class=card> <div class=card-header id=headinggeneral_haplotype_reconstruction> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#general_haplotype_reconstruction aria-expanded aria-controls=general_haplotype_reconstruction onclick="setAnchor('#general_haplotype_reconstruction')"><span class=property-name>haplotype_reconstruction</span></button> </h2> </div> <div id=general_haplotype_reconstruction class="collapse property-definition-div" aria-labelledby=headinggeneral_haplotype_reconstruction data-parent=#accordiongeneral_haplotype_reconstruction> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general onclick="anchorLink('general')">general</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general_haplotype_reconstruction onclick="anchorLink('general_haplotype_reconstruction')">haplotype_reconstruction</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "savage"</span><br> <span class=description><p>There are three options available for haplotype reconstruction, namely <a href=https://github.com/HaploConduct/HaploConduct/tree/master/savage>SAVAGE</a> <sup class=footnote-ref id=fnref-7><a href=#fn-7>1</a></sup>, <a href=https://github.com/cbg-ethz/haploclique>HaploClique</a> <sup class=footnote-ref id=fnref-8><a href=#fn-8>2</a></sup> or <a href=https://github.com/cbg-ethz/predicthaplo/ >PredictHaplo</a> <sup class=footnote-ref id=fnref-9><a href=#fn-9>3</a></sup>. SAVAGE is used by default. If you wish to use HaploClique, then indicate it in the configuration file as in the example.</p> <div class=footnotes> <hr> <ol> <li id=fn-7> <p>Baaijens, J. A. et al., De novo assembly of viral quasispecies using overlap graphs. Genome Res. 2017. <a href=#fnref-7 class=footnoteBackLink title="Jump back to footnote 1 in the text.">↩</a></p> </li> <li id=fn-8> <p>Töpfer, A. et al. Viral quasispecies assembly via maximal clique finding. PLOS Computational Biology. 2014. <a href=#fnref-8 class=footnoteBackLink title="Jump back to footnote 2 in the text.">↩</a></p> </li> <li id=fn-9> <p>Prabhakaran, S. et al. HIV haplotype inference using a propagating dirichlet process mixture model. IEEE/ACM transactions on computational biology and bioinformatics 11.1. 2013. <a href=#fnref-9 class=footnoteBackLink title="Jump back to footnote 3 in the text.">↩</a></p> </li> </ol> </div> </span><div class=enum-value id=general_haplotype_reconstruction_enum> <h4>Must be one of:</h4> <ul class=list-group><li class="list-group-item enum-item">"savage"</li><li class="list-group-item enum-item">"haploclique"</li><li class="list-group-item enum-item">"predicthaplo"</li></ul> </div> <br> <div class="badge badge-secondary">Example:</div> <br><div id=general_haplotype_reconstruction_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">haploclique</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiongeneral_threads> <div class=card> <div class=card-header id=headinggeneral_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#general_threads aria-expanded aria-controls=general_threads onclick="setAnchor('#general_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=general_threads class="collapse property-definition-div" aria-labelledby=headinggeneral_threads data-parent=#accordiongeneral_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general onclick="anchorLink('general')">general</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general_threads onclick="anchorLink('general_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1</span><br> <span class=description><p>This option should be used to specify the default number of threads for all multi-threaded rules. That is, unless the number of threads is specified for each rule, this value is set as default.</p> </span> <p><span class="badge badge-light restriction numeric-restriction" id=general_threads_number>Value must be greater or equal to <code>1</code></span></p> <br> <div class="badge badge-secondary">Example:</div> <br><div id=general_threads_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">4</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiongeneral_checksum> <div class=card> <div class=card-header id=headinggeneral_checksum> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#general_checksum aria-expanded aria-controls=general_checksum onclick="setAnchor('#general_checksum')"><span class=property-name>checksum</span></button> </h2> </div> <div id=general_checksum class="collapse property-definition-div" aria-labelledby=headinggeneral_checksum data-parent=#accordiongeneral_checksum> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general onclick="anchorLink('general')">general</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general_checksum onclick="anchorLink('general_checksum')">checksum</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "md5"</span><br> <span class=description><p>Sets the algorithm to be used when computing checksums for uploadable data.</p> </span><div class=enum-value id=general_checksum_enum> <h4>Must be one of:</h4> <ul class=list-group><li class="list-group-item enum-item">"md5"</li><li class="list-group-item enum-item">"sha1"</li><li class="list-group-item enum-item">"sha256"</li><li class="list-group-item enum-item">"sha224"</li><li class="list-group-item enum-item">"sha384"</li><li class="list-group-item enum-item">"sha512"</li><li class="list-group-item enum-item">"xxh64"</li><li class="list-group-item enum-item">"xxh32"</li><li class="list-group-item enum-item">"xxh128"</li></ul> </div> <br> <div class="badge badge-secondary">Example:</div> <br><div id=general_checksum_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">sha256</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiongeneral_temp_prefix> <div class=card> <div class=card-header id=headinggeneral_temp_prefix> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#general_temp_prefix aria-expanded aria-controls=general_temp_prefix onclick="setAnchor('#general_temp_prefix')"><span class=property-name>temp_prefix</span></button> </h2> </div> <div id=general_temp_prefix class="collapse property-definition-div" aria-labelledby=headinggeneral_temp_prefix data-parent=#accordiongeneral_temp_prefix> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general onclick="anchorLink('general')">general</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general_temp_prefix onclick="anchorLink('general_temp_prefix')">temp_prefix</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>Some step of V-pipe produce temporary files such as, e.g., decompressed intermediate — i.e. files which aren’t kept long-term but are deleted after all steps that needed them have finished. By default, these files are written in the output data directory. This option, makes it is possible to write them in a different directory instead. Use this option to, e.g., leverage a faster cluster-local storage or avoid wasting backup space on a snapshotted storage. You might want to consult the documentation provided by your HPC.</p> </span> <br> <div class="badge badge-secondary">Examples:</div> <br><div id=general_temp_prefix_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">temp</span><span class=w></span>
</pre></div> </div><div id=general_temp_prefix_ex2 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">/cluster/scratch</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiongeneral_tsvbased> <div class=card> <div class=card-header id=headinggeneral_tsvbased> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#general_tsvbased aria-expanded aria-controls=general_tsvbased onclick="setAnchor('#general_tsvbased')"><span class=property-name>tsvbased</span></button> </h2> </div> <div id=general_tsvbased class="collapse property-definition-div" aria-labelledby=headinggeneral_tsvbased data-parent=#accordiongeneral_tsvbased> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general onclick="anchorLink('general')">general</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general_tsvbased onclick="anchorLink('general_tsvbased')">tsvbased</a></div><span class="badge badge-dark value-type">Type: enum (of integer)</span> <span class="badge badge-success default-value">Default: 1</span><br> <span class=description><p>Specify whether TSV files like coverage and base counts should be 1-based (i.e.: the first base pair position is called <code>1</code>) like standard practice used in biology and most text formats such as VCF and GFF, or should be 0-based (i.e.: the first base pair position is called <code>0</code>) like in several Python tools such as pysam and the BED format.</p> <p>By default V-pipe uses 1-based TSV file (position column starts with <code>1</code>), but this option change the behaviour.</p> </span><div class=enum-value id=general_tsvbased_enum> <h4>Must be one of:</h4> <ul class=list-group><li class="list-group-item enum-item">0</li><li class="list-group-item enum-item">1</li></ul> </div> <br> <div class="badge badge-secondary">Example:</div> <br><div id=general_tsvbased_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">0</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiongeneral_id_separator> <div class=card> <div class=card-header id=headinggeneral_id_separator> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#general_id_separator aria-expanded aria-controls=general_id_separator onclick="setAnchor('#general_id_separator')"><span class=property-name>id_separator</span></button> </h2> </div> <div id=general_id_separator class="collapse property-definition-div" aria-labelledby=headinggeneral_id_separator data-parent=#accordiongeneral_id_separator> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general onclick="anchorLink('general')">general</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#general_id_separator onclick="anchorLink('general_id_separator')">id_separator</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "/"</span><br> <span class=description><p>Charater to use when assembling the two levels (e.g.: sample and a date), into a column title to be used in a report TSV file</p> <p>E.g., with this sample file</p> <pre><code>patient1 20100113
patient1 20110202
patient2 20081130
</code></pre> <p>the coverage TSV file’s column will be called <code>patient1/20100113</code>, <code>patient1/20110202</code> and <code>patient2/20081130</code>.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=general_id_separator_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="p p-Indicator">-</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput> <div class=card> <div class=card-header id=headinginput> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input aria-expanded aria-controls=input onclick="setAnchor('#input')"><span class=property-name>input</span></button> </h2> </div> <div id=input class="collapse property-definition-div" aria-labelledby=headinginput data-parent=#accordioninput> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <span class=description><p>Properties in this section of the configuration control the input of the pipeline.</p> </span> <div class=accordion id=accordioninput_datadir> <div class=card> <div class=card-header id=headinginput_datadir> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_datadir aria-expanded aria-controls=input_datadir onclick="setAnchor('#input_datadir')"><span class=property-name>datadir</span></button> </h2> </div> <div id=input_datadir class="collapse property-definition-div" aria-labelledby=headinginput_datadir data-parent=#accordioninput_datadir> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_datadir onclick="anchorLink('input_datadir')">datadir</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "samples/"</span><br> <span class=description><p>The input file for the workflow will be searched in this directory.</p> <p>V-pipe expects the input samples to be organized in a two-level directory hierarchy.</p> <ul> <li>The first level can be, e.g., patient samples or biological replicates of an experiment.</li> <li>The second level can be, e.g., different sampling dates or different sequencing runs of the same sample.</li> <li>Inside that directory, the sub-directory <code>raw_data</code> holds the sequencing data in FASTQ format (optionally compressed with GZip).</li> </ul> <p>For example:</p> <div class="highlight jumbotron"><pre><span></span><code>📁samples
├──📁patient1
│ ├──📁20100113
│ │ └──📁raw_data
│ │ ├──🧬patient1_20100113_R1.fastq
│ │ └──🧬patient1_20100113_R2.fastq
│ └──📁20110202
│ └──📁raw_data
│ ├──🧬patient1_20100202_R1.fastq
│ └──🧬patient1_20100202_R2.fastq
└──📁patient2
└──📁20081130
└──📁raw_data
├──🧬patient2_20081130_R1.fastq.gz
└──🧬patient2_20081130_R2.fastq.gz
</code></pre></div> </span> <br> <div class="badge badge-secondary">Examples:</div> <br><div id=input_datadir_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">tests/data/hiv/</span><span class=w></span>
</pre></div> </div><div id=input_datadir_ex2 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">tests/data/sars-cov-2/</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_paired> <div class=card> <div class=card-header id=headinginput_paired> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_paired aria-expanded aria-controls=input_paired onclick="setAnchor('#input_paired')"><span class=property-name>paired</span></button> </h2> </div> <div id=input_paired class="collapse property-definition-div" aria-labelledby=headinginput_paired data-parent=#accordioninput_paired> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_paired onclick="anchorLink('input_paired')">paired</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: true</span><br> <span class=description><p>Indicate whether the input sequencing reads correspond to paired-end reads.</p> <p>Paired-ended reads need to be in split files with <code>_R1</code> and <code>_R2</code> suffixes:</p> <div class="highlight jumbotron"><pre><span></span><code>📁raw_data
├──🧬patient2_20081130_R1.fastq.gz
└──🧬patient2_20081130_R2.fastq.gz
</code></pre></div> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=input_paired_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">False</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_fastq_suffix> <div class=card> <div class=card-header id=headinginput_fastq_suffix> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_fastq_suffix aria-expanded aria-controls=input_fastq_suffix onclick="setAnchor('#input_fastq_suffix')"><span class=property-name>fastq_suffix</span></button> </h2> </div> <div id=input_fastq_suffix class="collapse property-definition-div" aria-labelledby=headinginput_fastq_suffix data-parent=#accordioninput_fastq_suffix> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_fastq_suffix onclick="anchorLink('input_fastq_suffix')">fastq_suffix</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>V-pipe expects paired-end reads to be in files that end in <code>_R1</code> and <code>_R2</code> exactly right before the file extension, e.g., <code>_R1.fastq.gz</code>, because this is how the workflow finds and recognizes them.</p> <p>But Illumina’s bcl2fastq demultiplexer might introduce additional strings, e.g., <code>_R2_001.fast.gz</code> or, depending on its <em>mismatches</em> settings, e.g., <code>_R2_001_MM_1.fast.gz</code>. Use this options to specify anything which should go between the <code>_R1</code> and <code>_R2</code> endings and the file extension.</p> </span> <br> <div class="badge badge-secondary">Examples:</div> <br><div id=input_fastq_suffix_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">_001</span><span class=w></span>
</pre></div> </div><div id=input_fastq_suffix_ex2 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">_001_MM_1</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_samples_file> <div class=card> <div class=card-header id=headinginput_samples_file> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_samples_file aria-expanded aria-controls=input_samples_file onclick="setAnchor('#input_samples_file')"><span class=property-name>samples_file</span></button> </h2> </div> <div id=input_samples_file class="collapse property-definition-div" aria-labelledby=headinginput_samples_file data-parent=#accordioninput_samples_file> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_samples_file onclick="anchorLink('input_samples_file')">samples_file</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "config/samples.tsv"</span><br> <span class=description><p>File containing sample unique identifiers and dates as tab-separated values, e.g.,</p> <pre><code>patient1 20100113
patient1 20110202
patient2 20081130
</code></pre> <p>Here, we have two samples from patient 1 and one sample from patient 2. By default, V-pipe searches for a file named samples.tsv, if this file does not exist, a list of samples is built by globbing datadir directory contents.</p> <p>Optionally, the samples file can contain a third column specifying the read length. This is particularly useful when samples are sequenced using protocols with different read lengths.</p> <p>Optionally, a fourth column can contain a short name of a protocol (e.g.: <code>v3</code>) that is detailed in the file specified in <a href=#input_protocols_file><code>input</code> => <code>protocols_file</code></a>. This is useful if protocol details such as primers change over time, e.g. to adapt to new variants with SNV breaking primer binding affinity.</p> <p>Standardized Snakemake workflows place their tables inside the <code>config/</code> subdirectory, but using this options you can specify alternate locations, e.g., the current working directory (as done in legacy V-pipe v1.x/2.x).</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=input_samples_file_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">samples.tsv</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_protocols_file> <div class=card> <div class=card-header id=headinginput_protocols_file> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_protocols_file aria-expanded aria-controls=input_protocols_file onclick="setAnchor('#input_protocols_file')"><span class=property-name>protocols_file</span></button> </h2> </div> <div id=input_protocols_file class="collapse property-definition-div" aria-labelledby=headinginput_protocols_file data-parent=#accordioninput_protocols_file> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_protocols_file onclick="anchorLink('input_protocols_file')">protocols_file</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>When different samples have been processed with different library protocols, this file specifies a lookup table with per-protocol specific (primers bed and fasta), eg.:</p> <div class="highlight jumbotron"><pre><span></span><code><span class=nt>v41</span><span class=p>:</span><span class=w></span>
<span class=w> </span><span class=nt>name</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">SARS-CoV-2 ARTIC V4.1</span><span class=w></span>
<span class=w> </span><span class=nt>inserts_bedfile</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v41/SARS-CoV-2.insert.bed</span><span class=w></span>
<span class=w> </span><span class=nt>primers_bedfile</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v41/SARS-CoV-2.primer.bed</span><span class=w></span>
<span class=w> </span><span class=nt>primers_file</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v41/SARS-CoV-2.tsv</span><span class=w></span>
<span class=w> </span><span class=nt>primers_fasta</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v41/SARS-CoV-2.primer.fasta</span><span class=w></span>
<span class=nt>v4</span><span class=p>:</span><span class=w></span>
<span class=w> </span><span class=nt>name</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">SARS-CoV-2 ARTIC V4</span><span class=w></span>
<span class=w> </span><span class=nt>inserts_bedfile</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v4/SARS-CoV-2.insert.bed</span><span class=w></span>
<span class=w> </span><span class=nt>primers_bedfile</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v4/SARS-CoV-2.primer.bed</span><span class=w></span>
<span class=w> </span><span class=nt>primers_file</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v4/SARS-CoV-2.tsv</span><span class=w></span>
<span class=w> </span><span class=nt>primers_fasta</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v4/ARTIC_v4.fasta</span><span class=w></span>
<span class=nt>v3</span><span class=p>:</span><span class=w></span>
<span class=w> </span><span class=nt>name</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">SARS-CoV-2 ARTIC V3</span><span class=w></span>
<span class=w> </span><span class=nt>inserts_bedfile</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v3/nCoV-2019.insert.bed</span><span class=w></span>
<span class=w> </span><span class=nt>primers_bedfile</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v3/nCoV-2019.primer.bed</span><span class=w></span>
<span class=w> </span><span class=nt>primers_file</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v3/nCoV-2019.tsv</span><span class=w></span>
<span class=w> </span><span class=nt>primers_fasta</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">references/primers/v3/ARTIC_v3.fasta</span><span class=w></span>
</code></pre></div> <p>The short name can then be referenced in the <a href=#input_samples_file>samples TSV table file</a>:</p> <pre><code>sample_a 20211108 250 v3
sample_b 20220214 250 v4
</code></pre> <p><strong>Note</strong>: The virus-specific base configuration specified in <a href=#general_virus_base_config><code>general</code> => <code>virus_base_config</code></a> will most likely change this option’s default.<br> You are still free to override that default in your configuration shall the need arise.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=input_protocols_file_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/sars-cov-2/primers.yaml</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_read_length> <div class=card> <div class=card-header id=headinginput_read_length> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_read_length aria-expanded aria-controls=input_read_length onclick="setAnchor('#input_read_length')"><span class=property-name>read_length</span></button> </h2> </div> <div id=input_read_length class="collapse property-definition-div" aria-labelledby=headinginput_read_length data-parent=#accordioninput_read_length> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_read_length onclick="anchorLink('input_read_length')">read_length</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 250</span><br> <span class=description><p>Default for those samples whose read length isn’t specified explicitly in the optional third column of the <code>samples.tsv</code> table.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=input_read_length_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">100</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_primers_bedfile> <div class=card> <div class=card-header id=headinginput_primers_bedfile> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_primers_bedfile aria-expanded aria-controls=input_primers_bedfile onclick="setAnchor('#input_primers_bedfile')"><span class=property-name>primers_bedfile</span></button> </h2> </div> <div id=input_primers_bedfile class="collapse property-definition-div" aria-labelledby=headinginput_primers_bedfile data-parent=#accordioninput_primers_bedfile> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_primers_bedfile onclick="anchorLink('input_primers_bedfile')">primers_bedfile</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>A bed file with primers position to trim the alignment output</p> <p><strong>Note</strong>: The virus-specific base configuration specified in <a href=#general_virus_base_config><code>general</code> => <code>virus_base_config</code></a> will most likely change this option’s default.<br> You are still free to override that default in your configuration shall the need arise.</p> <p><strong>Note</strong>: individual sample can override this using the 4th column in the <a href=#input_samples_file>samples TSV table file</a> and the <a href=#input_protocols_file>protocols YAML look-up table</a>.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=input_primers_bedfile_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/sars-cov-2/primers/v3/nCoV-2019.primer.bed</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_inserts_bedfile> <div class=card> <div class=card-header id=headinginput_inserts_bedfile> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_inserts_bedfile aria-expanded aria-controls=input_inserts_bedfile onclick="setAnchor('#input_inserts_bedfile')"><span class=property-name>inserts_bedfile</span></button> </h2> </div> <div id=input_inserts_bedfile class="collapse property-definition-div" aria-labelledby=headinginput_inserts_bedfile data-parent=#accordioninput_inserts_bedfile> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_inserts_bedfile onclick="anchorLink('input_inserts_bedfile')">inserts_bedfile</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>A bed file with inserts position of the multiplex PCR output to use with amplicon-based analysis.</p> <p><strong>Note</strong>: The virus-specific base configuration specified in <a href=#general_virus_base_config><code>general</code> => <code>virus_base_config</code></a> will most likely change this option’s default.<br> You are still free to override that default in your configuration shall the need arise.</p> <p><strong>Note</strong>: individual sample can override this using the 4th column in the <a href=#input_samples_file>samples TSV table file</a> and the <a href=#input_protocols_file>protocols YAML look-up table</a>.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=input_inserts_bedfile_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/sars-cov-2/primers/v3/nCoV-2019.primer.bed</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_trim_percent_cutoff> <div class=card> <div class=card-header id=headinginput_trim_percent_cutoff> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_trim_percent_cutoff aria-expanded aria-controls=input_trim_percent_cutoff onclick="setAnchor('#input_trim_percent_cutoff')"><span class=property-name>trim_percent_cutoff</span></button> </h2> </div> <div id=input_trim_percent_cutoff class="collapse property-definition-div" aria-labelledby=headinginput_trim_percent_cutoff data-parent=#accordioninput_trim_percent_cutoff> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_trim_percent_cutoff onclick="anchorLink('input_trim_percent_cutoff')">trim_percent_cutoff</a></div><span class="badge badge-dark value-type">Type: number</span> <span class="badge badge-success default-value">Default: 0.8</span><br> <span class=description><p>Using this parameter, the user can specify the read-length threshold that should be applied during the quality trimming as a percentage (0 < <code>trim_percent_cutoff</code> < 1).</p> </span> <p><span class="badge badge-light restriction numeric-restriction" id=input_trim_percent_cutoff_number>Value must be greater or equal to <code>0</code> and lesser or equal to <code>1</code></span></p> <br> <div class="badge badge-secondary">Example:</div> <br><div id=input_trim_percent_cutoff_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">0.9</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_reference> <div class=card> <div class=card-header id=headinginput_reference> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_reference aria-expanded aria-controls=input_reference onclick="setAnchor('#input_reference')"><span class=property-name>reference</span></button> </h2> </div> <div id=input_reference class="collapse property-definition-div" aria-labelledby=headinginput_reference data-parent=#accordioninput_reference> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_reference onclick="anchorLink('input_reference')">reference</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "results/cohort_consensus.fasta"</span><br> <span class=description><p>Reference sequence to use for the alignment step</p> <p><strong>Note</strong>: The virus-specific base configuration specified in <a href=#general_virus_base_config><code>general</code> => <code>virus_base_config</code></a> will most likely change this option’s default to a reference for that virus.<br> You are still free to override that default in your configuration shall the need arise.</p> </span> <br> <div class="badge badge-secondary">Examples:</div> <br><div id=input_reference_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/hiv/HXB2.fasta</span><span class=w></span>
</pre></div> </div><div id=input_reference_ex2 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/sars-cov-2/NC_045512.2.fasta</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_gff_directory> <div class=card> <div class=card-header id=headinginput_gff_directory> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_gff_directory aria-expanded aria-controls=input_gff_directory onclick="setAnchor('#input_gff_directory')"><span class=property-name>gff_directory</span></button> </h2> </div> <div id=input_gff_directory class="collapse property-definition-div" aria-labelledby=headinginput_gff_directory data-parent=#accordioninput_gff_directory> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_gff_directory onclick="anchorLink('input_gff_directory')">gff_directory</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>A directory containing gff files that can be optionally used to annotate the reference genome in the visualization, e.g., with genes, mature products, protein domains, regions of interests, etc.</p> <p><strong>Note</strong>: The virus-specific base configuration specified in <a href=#general_virus_base_config><code>general</code> => <code>virus_base_config</code></a> will most likely change this option’s default.<br> You are still free to override that default in your configuration shall the need arise.</p> </span> <br> <div class="badge badge-secondary">Examples:</div> <br><div id=input_gff_directory_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/hiv/gffs/</span><span class=w></span>
</pre></div> </div><div id=input_gff_directory_ex2 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/sars-cov-2/gffs/</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_metainfo_file> <div class=card> <div class=card-header id=headinginput_metainfo_file> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_metainfo_file aria-expanded aria-controls=input_metainfo_file onclick="setAnchor('#input_metainfo_file')"><span class=property-name>metainfo_file</span></button> </h2> </div> <div id=input_metainfo_file class="collapse property-definition-div" aria-labelledby=headinginput_metainfo_file data-parent=#accordioninput_metainfo_file> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_metainfo_file onclick="anchorLink('input_metainfo_file')">metainfo_file</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>An associative array providing user-friendly name to display for each annotation .gff file in the <code>gff_directory</code></p> <p><strong>Note</strong>: The virus-specific base configuration specified in <a href=#general_virus_base_config><code>general</code> => <code>virus_base_config</code></a> will most likely change this option’s default.<br> You are still free to override that default in your configuration shall the need arise.</p> </span> <br> <div class="badge badge-secondary">Examples:</div> <br><div id=input_metainfo_file_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/hiv/metainfo.yaml</span><span class=w></span>
</pre></div> </div><div id=input_metainfo_file_ex2 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/sars-cov-2/metainfo.yaml</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_genes_gff> <div class=card> <div class=card-header id=headinginput_genes_gff> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_genes_gff aria-expanded aria-controls=input_genes_gff onclick="setAnchor('#input_genes_gff')"><span class=property-name>genes_gff</span></button> </h2> </div> <div id=input_genes_gff class="collapse property-definition-div" aria-labelledby=headinginput_genes_gff data-parent=#accordioninput_genes_gff> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_genes_gff onclick="anchorLink('input_genes_gff')">genes_gff</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>The specific annotation GFF file that has provides the <em>genes</em> position along the genome for reports that mention specific genes such frameshift-deletions-check.</p> <p><strong>Note</strong>: The virus-specific base configuration specified in <a href=#general_virus_base_config><code>general</code> => <code>virus_base_config</code></a> will most likely change this option’s default.<br> You are still free to override that default in your configuration shall the need arise.</p> <p><strong>Note</strong>: if not set, V-pipe will try auto-selecting a .gff file from the <code>gff_directory</code>.</p> </span> <br> <div class="badge badge-secondary">Examples:</div> <br><div id=input_genes_gff_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/hiv/gffs/GCF_000864765.1_ViralProj15476_genomic.gff</span><span class=w></span>
</pre></div> </div><div id=input_genes_gff_ex2 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/sars-cov-2/gffs/Genes_NC_045512.2.GFF3</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_primers_file> <div class=card> <div class=card-header id=headinginput_primers_file> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_primers_file aria-expanded aria-controls=input_primers_file onclick="setAnchor('#input_primers_file')"><span class=property-name>primers_file</span></button> </h2> </div> <div id=input_primers_file class="collapse property-definition-div" aria-labelledby=headinginput_primers_file data-parent=#accordioninput_primers_file> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_primers_file onclick="anchorLink('input_primers_file')">primers_file</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>A table with primers to display on the visualization</p> <p><strong>Note</strong>: The virus-specific base configuration specified in <a href=#general_virus_base_config><code>general</code> => <code>virus_base_config</code></a> will most likely change this option’s default.<br> You are still free to override that default in your configuration shall the need arise.</p> <p><strong>Note</strong>: individual sample can override this using the 4th column in the <a href=#input_samples_file>samples TSV table file</a> and the <a href=#input_protocols_file>protocols YAML look-up table</a>.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=input_primers_file_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/sars-cov-2/primers/v3/nCoV-2019.tsv</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_variants_def_directory> <div class=card> <div class=card-header id=headinginput_variants_def_directory> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_variants_def_directory aria-expanded aria-controls=input_variants_def_directory onclick="setAnchor('#input_variants_def_directory')"><span class=property-name>variants_def_directory</span></button> </h2> </div> <div id=input_variants_def_directory class="collapse property-definition-div" aria-labelledby=headinginput_variants_def_directory data-parent=#accordioninput_variants_def_directory> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_variants_def_directory onclick="anchorLink('input_variants_def_directory')">variants_def_directory</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>Directory holding a list of COJAC YAML definitions of variants of concern that will be used for search of variant signatures</p> <p><strong>Note</strong>: The virus-specific base configuration specified in <a href=#general_virus_base_config><code>general</code> => <code>virus_base_config</code></a> will most likely change this option’s default.<br> You are still free to override that default in your configuration shall the need arise.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=input_variants_def_directory_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/sars-cov-2/voc/</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninput_phylogeny_data> <div class=card> <div class=card-header id=headinginput_phylogeny_data> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#input_phylogeny_data aria-expanded aria-controls=input_phylogeny_data onclick="setAnchor('#input_phylogeny_data')"><span class=property-name>phylogeny_data</span></button> </h2> </div> <div id=input_phylogeny_data class="collapse property-definition-div" aria-labelledby=headinginput_phylogeny_data data-parent=#accordioninput_phylogeny_data> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input onclick="anchorLink('input')">input</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#input_phylogeny_data onclick="anchorLink('input_phylogeny_data')">phylogeny_data</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>A FASTQ file with sequences of interest</p> <p><strong>Note</strong>: These sequences are used, together with the consensus sequence, to build a phylogenetic tree.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=input_phylogeny_data_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/sars-cov-2/phylogeny/selected_covid_sequences.fasta</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionoutput> <div class=card> <div class=card-header id=headingoutput> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#output aria-expanded aria-controls=output onclick="setAnchor('#output')"><span class=property-name>output</span></button> </h2> </div> <div id=output class="collapse property-definition-div" aria-labelledby=headingoutput data-parent=#accordionoutput> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output onclick="anchorLink('output')">output</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <span class=description><p>Properties in this section of the configuration control the output of the pipeline.</p> </span> <div class=accordion id=accordionoutput_datadir> <div class=card> <div class=card-header id=headingoutput_datadir> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#output_datadir aria-expanded aria-controls=output_datadir onclick="setAnchor('#output_datadir')"><span class=property-name>datadir</span></button> </h2> </div> <div id=output_datadir class="collapse property-definition-div" aria-labelledby=headingoutput_datadir data-parent=#accordionoutput_datadir> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output onclick="anchorLink('output')">output</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output_datadir onclick="anchorLink('output_datadir')">datadir</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "results"</span><br> <span class=description><p>The workflow will write its output files into this directory. This will follow the same structure as for the input.</p> <p>For each sample, V-pipe produces several output files that are located in the corresponding sample-specific directory. First, the alignment file and consensus sequences are located in the <code>alignments</code> and <code>references</code> subdirectories, respectively. Second, output files containing SNVs and viral haplotypes are located in the <code>variants</code> subdirectories.</p> <p>Using the sample example as in the <a href=#input_datadir><code>input</code></a> section, the output files for the two patient samples will be located in the following subdirectories:</p> <div class="highlight jumbotron"><pre><span></span><code>📁results
├──📁patient1
│ ├──📁20100113
│ │ ├──📁alignments
│ │ | └──REF_aln.bam
│ │ ├──📁references
| | | ├──consensus.bcftools.fasta
| | | ├──ref_ambig.fasta
| | | └──ref_majority.fasta
| | └──📁variants
| | ├──📁SNVs
| | | └──snvs.vcf
| | └──📁global
| | └──contigs_stage_c.fasta
│ └──📁20110202
│ ├──📁alignments
│ | └──REF_aln.bam
│ ├──📁references
| | ├──consensus.bcftools.fasta
| | ├──ref_ambig.fasta
| | └──ref_majority.fasta
| └──📁variants
| ├──📁SNVs
| | └──snvs.vcf
| └──📁global
| └──contigs_stage_c.fasta
└─📁patient2
├──📁alignments
| └──REF_aln.bam
├──📁references
| ├──consensus.bcftools.fasta
| ├──ref_ambig.fasta
| └──ref_majority.fasta
└──📁variants
├──📁SNVs
| └──snvs.vcf
└──📁global
└──contigs_stage_c.fasta
</code></pre></div> <ul> <li>Standardized Snakemake workflows place their output in a <code>results</code> subdirectory</li> <li>If your prefer the output written, e.g., to the same <code>samples/</code> subdirectory as the input (as used to be done in legacy V-pipe v1.x/2.x), you can use this options you can specify alternate target locations.</li> </ul> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=output_datadir_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">samples</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionoutput_cohortdir> <div class=card> <div class=card-header id=headingoutput_cohortdir> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#output_cohortdir aria-expanded aria-controls=output_cohortdir onclick="setAnchor('#output_cohortdir')"><span class=property-name>cohortdir</span></button> </h2> </div> <div id=output_cohortdir class="collapse property-definition-div" aria-labelledby=headingoutput_cohortdir data-parent=#accordionoutput_cohortdir> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output onclick="anchorLink('output')">output</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output_cohortdir onclick="anchorLink('output_cohortdir')">cohortdir</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>In addition, V-pipe can optionally generate a few cohort-wide results, such as a current cohort consensus fasta file, or a TSV file containing the frequencies of all minor alleles that differ from the consensus among analyzed samples.<br> By default, these output files are located at the base of the <a href=#output_datadir><code>output</code> <code>datadir</code></a>, outside of the two-level per sample structure:</p> <div class="highlight jumbotron"><pre><span></span><code><span class=go>results</span>
<span class=go>├──minority_variants.tsv</span>
<span class=go>├──cohort_consensus.fasta</span>
<span class=go>├──patient1</span>
<span class=go>│ ├──20100113</span>
<span class=go>│ │ ├──alignments</span>
<span class=go>…</span>
</code></pre></div> <p>If you prefer instead, e.g., such cohort-wide results behind written in a subdirectory of the working directory at the same level as the <code>datadir</code>s, you can use this options you can specify alternate subdirectory relative to the <code>datadir</code> property. (Use <code>..</code> prefix if you want instead your cohort-wide results to be in a directory at the sample level as <code>samples/</code> and <code>results/</code>. See the example below to recreate the <code>variants/</code> directory used by legacy V-pipe v1.x/2.x).</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=output_cohortdir_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">../variants</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionoutput_QA> <div class=card> <div class=card-header id=headingoutput_QA> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#output_QA aria-expanded aria-controls=output_QA onclick="setAnchor('#output_QA')"><span class=property-name>QA</span></button> </h2> </div> <div id=output_QA class="collapse property-definition-div" aria-labelledby=headingoutput_QA data-parent=#accordionoutput_QA> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output onclick="anchorLink('output')">output</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output_QA onclick="anchorLink('output_QA')">QA</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>V-pipe can produce several outputs to assess the quality of the output of its steps, e.g., checking whether a sample’s consensus sequence generated by bctfools does result in frameshifting indels and writing a report in sample’s <code>…/references/frameshift_deletions_check.tsv</code>. Such reports can be useful when submitting sequences to GISAID.</p> <p>This option turns on such QA features.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=output_QA_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionoutput_trim_primers> <div class=card> <div class=card-header id=headingoutput_trim_primers> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#output_trim_primers aria-expanded aria-controls=output_trim_primers onclick="setAnchor('#output_trim_primers')"><span class=property-name>trim_primers</span></button> </h2> </div> <div id=output_trim_primers class="collapse property-definition-div" aria-labelledby=headingoutput_trim_primers data-parent=#accordionoutput_trim_primers> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output onclick="anchorLink('output')">output</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output_trim_primers onclick="anchorLink('output_trim_primers')">trim_primers</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>This option indicates that the samples come from PCR amplification and the primers should be trimmed from amplicons in the alignment file. The trimmed read are written to each sample’s <code>…/variants/SNVs/REF_aln_trim.bam</code>.</p> <p>Using this option requires either specifying a primers bed file in <a href=#input_primers_bedfile><code>input</code> => <code>protocols_file</code></a>, or using a <a href=#input_samples_file>4 column input samples TSV file</a> and specify a protocol look-up YAML file in <a href=#input_protocols_file><code>input</code> => <code>protocols_file</code></a>.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=output_trim_primers_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionoutput_snv> <div class=card> <div class=card-header id=headingoutput_snv> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#output_snv aria-expanded aria-controls=output_snv onclick="setAnchor('#output_snv')"><span class=property-name>snv</span></button> </h2> </div> <div id=output_snv class="collapse property-definition-div" aria-labelledby=headingoutput_snv data-parent=#accordionoutput_snv> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output onclick="anchorLink('output')">output</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output_snv onclick="anchorLink('output_snv')">snv</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>This option selects whether the SNV caller step should be executed and its output written to each sample’s <code>…/variants/SNVs/snvs.csv</code>.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=output_snv_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionoutput_local> <div class=card> <div class=card-header id=headingoutput_local> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#output_local aria-expanded aria-controls=output_local onclick="setAnchor('#output_local')"><span class=property-name>local</span></button> </h2> </div> <div id=output_local class="collapse property-definition-div" aria-labelledby=headingoutput_local data-parent=#accordionoutput_local> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output onclick="anchorLink('output')">output</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output_local onclick="anchorLink('output_local')">local</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>This option activates local haplotype reconstruction (only available when using ShoRAH or VILOCA).</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=output_local_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionoutput_global> <div class=card> <div class=card-header id=headingoutput_global> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#output_global aria-expanded aria-controls=output_global onclick="setAnchor('#output_global')"><span class=property-name>global</span></button> </h2> </div> <div id=output_global class="collapse property-definition-div" aria-labelledby=headingoutput_global data-parent=#accordionoutput_global> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output onclick="anchorLink('output')">output</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output_global onclick="anchorLink('output_global')">global</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>This option turns on global haplotype reconstruction.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=output_global_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionoutput_visualization> <div class=card> <div class=card-header id=headingoutput_visualization> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#output_visualization aria-expanded aria-controls=output_visualization onclick="setAnchor('#output_visualization')"><span class=property-name>visualization</span></button> </h2> </div> <div id=output_visualization class="collapse property-definition-div" aria-labelledby=headingoutput_visualization data-parent=#accordionoutput_visualization> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output onclick="anchorLink('output')">output</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output_visualization onclick="anchorLink('output_visualization')">visualization</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>This option selects whether to generate HTML visualization of the SNVs in each sample’s <code>…/visualization/index.html</code>.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=output_visualization_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionoutput_diversity> <div class=card> <div class=card-header id=headingoutput_diversity> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#output_diversity aria-expanded aria-controls=output_diversity onclick="setAnchor('#output_diversity')"><span class=property-name>diversity</span></button> </h2> </div> <div id=output_diversity class="collapse property-definition-div" aria-labelledby=headingoutput_diversity data-parent=#accordionoutput_diversity> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output onclick="anchorLink('output')">output</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output_diversity onclick="anchorLink('output_diversity')">diversity</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>This option turns on the computation of diversity measures in each sample.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=output_diversity_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionoutput_dehumanized_raw_reads> <div class=card> <div class=card-header id=headingoutput_dehumanized_raw_reads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#output_dehumanized_raw_reads aria-expanded aria-controls=output_dehumanized_raw_reads onclick="setAnchor('#output_dehumanized_raw_reads')"><span class=property-name>dehumanized_raw_reads</span></button> </h2> </div> <div id=output_dehumanized_raw_reads class="collapse property-definition-div" aria-labelledby=headingoutput_dehumanized_raw_reads data-parent=#accordionoutput_dehumanized_raw_reads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output onclick="anchorLink('output')">output</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output_dehumanized_raw_reads onclick="anchorLink('output_dehumanized_raw_reads')">dehumanized_raw_reads</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>This option turns on dehumanization of the raw reads (i.e. removal of host’s reads) and generates the file <code>dehuman.cram</code>. This is useful to prepare raw reads for upload on public databases such as, e.g. ENA (European Nucleotide Archive).</p> <p>This only applies to the upload and does not affect the main workflow.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=output_dehumanized_raw_reads_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionoutput_upload> <div class=card> <div class=card-header id=headingoutput_upload> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#output_upload aria-expanded aria-controls=output_upload onclick="setAnchor('#output_upload')"><span class=property-name>upload</span></button> </h2> </div> <div id=output_upload class="collapse property-definition-div" aria-labelledby=headingoutput_upload data-parent=#accordionoutput_upload> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output onclick="anchorLink('output')">output</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#output_upload onclick="anchorLink('output_upload')">upload</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>This option can be used for assistance in incremental upload of data. See section <code>upload</code> for an example.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=output_upload_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionapplications> <div class=card> <div class=card-header id=headingapplications> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications aria-expanded aria-controls=applications onclick="setAnchor('#applications')"><span class=property-name>applications</span></button> </h2> </div> <div id=applications class="collapse property-definition-div" aria-labelledby=headingapplications data-parent=#accordionapplications> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <span class=description><p>The path to the different software packages can be specified using this section.</p> <p>It is especially useful when dependencies are not obtained via conda such as VICUNA, and when the software packages are not in the <code>PATH</code>.</p> <p><strong>Note</strong> we strongly recommend to use conda environments, by adding the <code>--use-conda</code> flag to the V-pipe execution command, e.g. <code>./vpipe --use-conda</code>. If you prefer to use your own installations, this section allows you to specify the location of the executable files.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=applications_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class=nt>bwa</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">/path/to/bwa</span><span class=w></span>
<span class=nt>haploclique</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">/path/to/haploclique</span><span class=w></span>
</pre></div> </div> <div class=accordion id=accordionapplications_gunzip> <div class=card> <div class=card-header id=headingapplications_gunzip> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_gunzip aria-expanded aria-controls=applications_gunzip onclick="setAnchor('#applications_gunzip')"><span class=property-name>gunzip</span></button> </h2> </div> <div id=applications_gunzip class="collapse property-definition-div" aria-labelledby=headingapplications_gunzip data-parent=#accordionapplications_gunzip> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_gunzip onclick="anchorLink('applications_gunzip')">gunzip</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "gunzip"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_zstd> <div class=card> <div class=card-header id=headingapplications_zstd> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_zstd aria-expanded aria-controls=applications_zstd onclick="setAnchor('#applications_zstd')"><span class=property-name>zstd</span></button> </h2> </div> <div id=applications_zstd class="collapse property-definition-div" aria-labelledby=headingapplications_zstd data-parent=#accordionapplications_zstd> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_zstd onclick="anchorLink('applications_zstd')">zstd</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "zstd"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_xsv> <div class=card> <div class=card-header id=headingapplications_xsv> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_xsv aria-expanded aria-controls=applications_xsv onclick="setAnchor('#applications_xsv')"><span class=property-name>xsv</span></button> </h2> </div> <div id=applications_xsv class="collapse property-definition-div" aria-labelledby=headingapplications_xsv data-parent=#accordionapplications_xsv> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_xsv onclick="anchorLink('applications_xsv')">xsv</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "xsv"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_prinseq> <div class=card> <div class=card-header id=headingapplications_prinseq> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_prinseq aria-expanded aria-controls=applications_prinseq onclick="setAnchor('#applications_prinseq')"><span class=property-name>prinseq</span></button> </h2> </div> <div id=applications_prinseq class="collapse property-definition-div" aria-labelledby=headingapplications_prinseq data-parent=#accordionapplications_prinseq> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_prinseq onclick="anchorLink('applications_prinseq')">prinseq</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "prinseq-lite.pl"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_fastqc> <div class=card> <div class=card-header id=headingapplications_fastqc> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_fastqc aria-expanded aria-controls=applications_fastqc onclick="setAnchor('#applications_fastqc')"><span class=property-name>fastqc</span></button> </h2> </div> <div id=applications_fastqc class="collapse property-definition-div" aria-labelledby=headingapplications_fastqc data-parent=#accordionapplications_fastqc> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_fastqc onclick="anchorLink('applications_fastqc')">fastqc</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "fastqc"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_vicuna> <div class=card> <div class=card-header id=headingapplications_vicuna> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_vicuna aria-expanded aria-controls=applications_vicuna onclick="setAnchor('#applications_vicuna')"><span class=property-name>vicuna</span></button> </h2> </div> <div id=applications_vicuna class="collapse property-definition-div" aria-labelledby=headingapplications_vicuna data-parent=#accordionapplications_vicuna> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_vicuna onclick="anchorLink('applications_vicuna')">vicuna</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "vicuna"</span><br> <span class=description><p>Due to a special license, VICUNA is <strong>not</strong> available from bioconda and must be installed from <a href=https://www.broadinstitute.org/viral-genomics/vicuna>its original website</a>.<br> Use this option to specify where you have installed its executable.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionapplications_indelfixer> <div class=card> <div class=card-header id=headingapplications_indelfixer> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_indelfixer aria-expanded aria-controls=applications_indelfixer onclick="setAnchor('#applications_indelfixer')"><span class=property-name>indelfixer</span></button> </h2> </div> <div id=applications_indelfixer class="collapse property-definition-div" aria-labelledby=headingapplications_indelfixer data-parent=#accordionapplications_indelfixer> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_indelfixer onclick="anchorLink('applications_indelfixer')">indelfixer</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "InDelFixer"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_consensusfixer> <div class=card> <div class=card-header id=headingapplications_consensusfixer> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_consensusfixer aria-expanded aria-controls=applications_consensusfixer onclick="setAnchor('#applications_consensusfixer')"><span class=property-name>consensusfixer</span></button> </h2> </div> <div id=applications_consensusfixer class="collapse property-definition-div" aria-labelledby=headingapplications_consensusfixer data-parent=#accordionapplications_consensusfixer> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_consensusfixer onclick="anchorLink('applications_consensusfixer')">consensusfixer</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "ConsensusFixer"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_picard> <div class=card> <div class=card-header id=headingapplications_picard> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_picard aria-expanded aria-controls=applications_picard onclick="setAnchor('#applications_picard')"><span class=property-name>picard</span></button> </h2> </div> <div id=applications_picard class="collapse property-definition-div" aria-labelledby=headingapplications_picard data-parent=#accordionapplications_picard> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_picard onclick="anchorLink('applications_picard')">picard</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "picard"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_bwa> <div class=card> <div class=card-header id=headingapplications_bwa> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_bwa aria-expanded aria-controls=applications_bwa onclick="setAnchor('#applications_bwa')"><span class=property-name>bwa</span></button> </h2> </div> <div id=applications_bwa class="collapse property-definition-div" aria-labelledby=headingapplications_bwa data-parent=#accordionapplications_bwa> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_bwa onclick="anchorLink('applications_bwa')">bwa</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "bwa"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_bowtie_idx> <div class=card> <div class=card-header id=headingapplications_bowtie_idx> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_bowtie_idx aria-expanded aria-controls=applications_bowtie_idx onclick="setAnchor('#applications_bowtie_idx')"><span class=property-name>bowtie_idx</span></button> </h2> </div> <div id=applications_bowtie_idx class="collapse property-definition-div" aria-labelledby=headingapplications_bowtie_idx data-parent=#accordionapplications_bowtie_idx> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_bowtie_idx onclick="anchorLink('applications_bowtie_idx')">bowtie_idx</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "bowtie2-build"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_bowtie> <div class=card> <div class=card-header id=headingapplications_bowtie> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_bowtie aria-expanded aria-controls=applications_bowtie onclick="setAnchor('#applications_bowtie')"><span class=property-name>bowtie</span></button> </h2> </div> <div id=applications_bowtie class="collapse property-definition-div" aria-labelledby=headingapplications_bowtie data-parent=#accordionapplications_bowtie> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_bowtie onclick="anchorLink('applications_bowtie')">bowtie</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "bowtie2"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_minimap> <div class=card> <div class=card-header id=headingapplications_minimap> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_minimap aria-expanded aria-controls=applications_minimap onclick="setAnchor('#applications_minimap')"><span class=property-name>minimap</span></button> </h2> </div> <div id=applications_minimap class="collapse property-definition-div" aria-labelledby=headingapplications_minimap data-parent=#accordionapplications_minimap> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_minimap onclick="anchorLink('applications_minimap')">minimap</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "minimap2"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_samtools> <div class=card> <div class=card-header id=headingapplications_samtools> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_samtools aria-expanded aria-controls=applications_samtools onclick="setAnchor('#applications_samtools')"><span class=property-name>samtools</span></button> </h2> </div> <div id=applications_samtools class="collapse property-definition-div" aria-labelledby=headingapplications_samtools data-parent=#accordionapplications_samtools> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_samtools onclick="anchorLink('applications_samtools')">samtools</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "samtools"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_extract_consensus> <div class=card> <div class=card-header id=headingapplications_extract_consensus> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_extract_consensus aria-expanded aria-controls=applications_extract_consensus onclick="setAnchor('#applications_extract_consensus')"><span class=property-name>extract_consensus</span></button> </h2> </div> <div id=applications_extract_consensus class="collapse property-definition-div" aria-labelledby=headingapplications_extract_consensus data-parent=#accordionapplications_extract_consensus> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_extract_consensus onclick="anchorLink('applications_extract_consensus')">extract_consensus</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "extract_consensus"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_matcher> <div class=card> <div class=card-header id=headingapplications_matcher> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_matcher aria-expanded aria-controls=applications_matcher onclick="setAnchor('#applications_matcher')"><span class=property-name>matcher</span></button> </h2> </div> <div id=applications_matcher class="collapse property-definition-div" aria-labelledby=headingapplications_matcher data-parent=#accordionapplications_matcher> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_matcher onclick="anchorLink('applications_matcher')">matcher</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "matcher"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_frameshift_deletions_checks> <div class=card> <div class=card-header id=headingapplications_frameshift_deletions_checks> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_frameshift_deletions_checks aria-expanded aria-controls=applications_frameshift_deletions_checks onclick="setAnchor('#applications_frameshift_deletions_checks')"><span class=property-name>frameshift_deletions_checks</span></button> </h2> </div> <div id=applications_frameshift_deletions_checks class="collapse property-definition-div" aria-labelledby=headingapplications_frameshift_deletions_checks data-parent=#accordionapplications_frameshift_deletions_checks> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_frameshift_deletions_checks onclick="anchorLink('applications_frameshift_deletions_checks')">frameshift_deletions_checks</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "frameshift_deletions_checks"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_paired_end_read_merger> <div class=card> <div class=card-header id=headingapplications_paired_end_read_merger> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_paired_end_read_merger aria-expanded aria-controls=applications_paired_end_read_merger onclick="setAnchor('#applications_paired_end_read_merger')"><span class=property-name>paired_end_read_merger</span></button> </h2> </div> <div id=applications_paired_end_read_merger class="collapse property-definition-div" aria-labelledby=headingapplications_paired_end_read_merger data-parent=#accordionapplications_paired_end_read_merger> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_paired_end_read_merger onclick="anchorLink('applications_paired_end_read_merger')">paired_end_read_merger</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "paired_end_read_merger"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_mafft> <div class=card> <div class=card-header id=headingapplications_mafft> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_mafft aria-expanded aria-controls=applications_mafft onclick="setAnchor('#applications_mafft')"><span class=property-name>mafft</span></button> </h2> </div> <div id=applications_mafft class="collapse property-definition-div" aria-labelledby=headingapplications_mafft data-parent=#accordionapplications_mafft> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_mafft onclick="anchorLink('applications_mafft')">mafft</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "mafft"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_ngshmmalign> <div class=card> <div class=card-header id=headingapplications_ngshmmalign> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_ngshmmalign aria-expanded aria-controls=applications_ngshmmalign onclick="setAnchor('#applications_ngshmmalign')"><span class=property-name>ngshmmalign</span></button> </h2> </div> <div id=applications_ngshmmalign class="collapse property-definition-div" aria-labelledby=headingapplications_ngshmmalign data-parent=#accordionapplications_ngshmmalign> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_ngshmmalign onclick="anchorLink('applications_ngshmmalign')">ngshmmalign</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "ngshmmalign"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_convert_reference> <div class=card> <div class=card-header id=headingapplications_convert_reference> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_convert_reference aria-expanded aria-controls=applications_convert_reference onclick="setAnchor('#applications_convert_reference')"><span class=property-name>convert_reference</span></button> </h2> </div> <div id=applications_convert_reference class="collapse property-definition-div" aria-labelledby=headingapplications_convert_reference data-parent=#accordionapplications_convert_reference> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_convert_reference onclick="anchorLink('applications_convert_reference')">convert_reference</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "convert_reference"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_extract_seq> <div class=card> <div class=card-header id=headingapplications_extract_seq> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_extract_seq aria-expanded aria-controls=applications_extract_seq onclick="setAnchor('#applications_extract_seq')"><span class=property-name>extract_seq</span></button> </h2> </div> <div id=applications_extract_seq class="collapse property-definition-div" aria-labelledby=headingapplications_extract_seq data-parent=#accordionapplications_extract_seq> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_extract_seq onclick="anchorLink('applications_extract_seq')">extract_seq</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "extract_seq"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_coverage_stats> <div class=card> <div class=card-header id=headingapplications_coverage_stats> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_coverage_stats aria-expanded aria-controls=applications_coverage_stats onclick="setAnchor('#applications_coverage_stats')"><span class=property-name>coverage_stats</span></button> </h2> </div> <div id=applications_coverage_stats class="collapse property-definition-div" aria-labelledby=headingapplications_coverage_stats data-parent=#accordionapplications_coverage_stats> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_coverage_stats onclick="anchorLink('applications_coverage_stats')">coverage_stats</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "coverage_stats"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_remove_gaps_msa> <div class=card> <div class=card-header id=headingapplications_remove_gaps_msa> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_remove_gaps_msa aria-expanded aria-controls=applications_remove_gaps_msa onclick="setAnchor('#applications_remove_gaps_msa')"><span class=property-name>remove_gaps_msa</span></button> </h2> </div> <div id=applications_remove_gaps_msa class="collapse property-definition-div" aria-labelledby=headingapplications_remove_gaps_msa data-parent=#accordionapplications_remove_gaps_msa> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_remove_gaps_msa onclick="anchorLink('applications_remove_gaps_msa')">remove_gaps_msa</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "remove_gaps_msa"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_ivar> <div class=card> <div class=card-header id=headingapplications_ivar> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_ivar aria-expanded aria-controls=applications_ivar onclick="setAnchor('#applications_ivar')"><span class=property-name>ivar</span></button> </h2> </div> <div id=applications_ivar class="collapse property-definition-div" aria-labelledby=headingapplications_ivar data-parent=#accordionapplications_ivar> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_ivar onclick="anchorLink('applications_ivar')">ivar</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "ivar"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_aln2basecnt> <div class=card> <div class=card-header id=headingapplications_aln2basecnt> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_aln2basecnt aria-expanded aria-controls=applications_aln2basecnt onclick="setAnchor('#applications_aln2basecnt')"><span class=property-name>aln2basecnt</span></button> </h2> </div> <div id=applications_aln2basecnt class="collapse property-definition-div" aria-labelledby=headingapplications_aln2basecnt data-parent=#accordionapplications_aln2basecnt> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_aln2basecnt onclick="anchorLink('applications_aln2basecnt')">aln2basecnt</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "aln2basecnt"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_gather_coverage> <div class=card> <div class=card-header id=headingapplications_gather_coverage> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_gather_coverage aria-expanded aria-controls=applications_gather_coverage onclick="setAnchor('#applications_gather_coverage')"><span class=property-name>gather_coverage</span></button> </h2> </div> <div id=applications_gather_coverage class="collapse property-definition-div" aria-labelledby=headingapplications_gather_coverage data-parent=#accordionapplications_gather_coverage> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_gather_coverage onclick="anchorLink('applications_gather_coverage')">gather_coverage</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "gather_coverage"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_minority_freq> <div class=card> <div class=card-header id=headingapplications_minority_freq> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_minority_freq aria-expanded aria-controls=applications_minority_freq onclick="setAnchor('#applications_minority_freq')"><span class=property-name>minority_freq</span></button> </h2> </div> <div id=applications_minority_freq class="collapse property-definition-div" aria-labelledby=headingapplications_minority_freq data-parent=#accordionapplications_minority_freq> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_minority_freq onclick="anchorLink('applications_minority_freq')">minority_freq</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "minority_freq"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_extract_coverage_intervals> <div class=card> <div class=card-header id=headingapplications_extract_coverage_intervals> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_extract_coverage_intervals aria-expanded aria-controls=applications_extract_coverage_intervals onclick="setAnchor('#applications_extract_coverage_intervals')"><span class=property-name>extract_coverage_intervals</span></button> </h2> </div> <div id=applications_extract_coverage_intervals class="collapse property-definition-div" aria-labelledby=headingapplications_extract_coverage_intervals data-parent=#accordionapplications_extract_coverage_intervals> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_extract_coverage_intervals onclick="anchorLink('applications_extract_coverage_intervals')">extract_coverage_intervals</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "extract_coverage_intervals"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_shorah> <div class=card> <div class=card-header id=headingapplications_shorah> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_shorah aria-expanded aria-controls=applications_shorah onclick="setAnchor('#applications_shorah')"><span class=property-name>shorah</span></button> </h2> </div> <div id=applications_shorah class="collapse property-definition-div" aria-labelledby=headingapplications_shorah data-parent=#accordionapplications_shorah> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_shorah onclick="anchorLink('applications_shorah')">shorah</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "shorah shotgun"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_viloca> <div class=card> <div class=card-header id=headingapplications_viloca> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_viloca aria-expanded aria-controls=applications_viloca onclick="setAnchor('#applications_viloca')"><span class=property-name>viloca</span></button> </h2> </div> <div id=applications_viloca class="collapse property-definition-div" aria-labelledby=headingapplications_viloca data-parent=#accordionapplications_viloca> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_viloca onclick="anchorLink('applications_viloca')">viloca</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "viloca run"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_lofreq> <div class=card> <div class=card-header id=headingapplications_lofreq> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_lofreq aria-expanded aria-controls=applications_lofreq onclick="setAnchor('#applications_lofreq')"><span class=property-name>lofreq</span></button> </h2> </div> <div id=applications_lofreq class="collapse property-definition-div" aria-labelledby=headingapplications_lofreq data-parent=#accordionapplications_lofreq> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_lofreq onclick="anchorLink('applications_lofreq')">lofreq</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "lofreq"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_bcftools> <div class=card> <div class=card-header id=headingapplications_bcftools> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_bcftools aria-expanded aria-controls=applications_bcftools onclick="setAnchor('#applications_bcftools')"><span class=property-name>bcftools</span></button> </h2> </div> <div id=applications_bcftools class="collapse property-definition-div" aria-labelledby=headingapplications_bcftools data-parent=#accordionapplications_bcftools> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_bcftools onclick="anchorLink('applications_bcftools')">bcftools</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "bcftools"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_haploclique> <div class=card> <div class=card-header id=headingapplications_haploclique> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_haploclique aria-expanded aria-controls=applications_haploclique onclick="setAnchor('#applications_haploclique')"><span class=property-name>haploclique</span></button> </h2> </div> <div id=applications_haploclique class="collapse property-definition-div" aria-labelledby=headingapplications_haploclique data-parent=#accordionapplications_haploclique> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_haploclique onclick="anchorLink('applications_haploclique')">haploclique</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "haploclique"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_compute_mds> <div class=card> <div class=card-header id=headingapplications_compute_mds> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_compute_mds aria-expanded aria-controls=applications_compute_mds onclick="setAnchor('#applications_compute_mds')"><span class=property-name>compute_mds</span></button> </h2> </div> <div id=applications_compute_mds class="collapse property-definition-div" aria-labelledby=headingapplications_compute_mds data-parent=#accordionapplications_compute_mds> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_compute_mds onclick="anchorLink('applications_compute_mds')">compute_mds</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "compute_mds"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_savage> <div class=card> <div class=card-header id=headingapplications_savage> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_savage aria-expanded aria-controls=applications_savage onclick="setAnchor('#applications_savage')"><span class=property-name>savage</span></button> </h2> </div> <div id=applications_savage class="collapse property-definition-div" aria-labelledby=headingapplications_savage data-parent=#accordionapplications_savage> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_savage onclick="anchorLink('applications_savage')">savage</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "savage"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_predicthaplo> <div class=card> <div class=card-header id=headingapplications_predicthaplo> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_predicthaplo aria-expanded aria-controls=applications_predicthaplo onclick="setAnchor('#applications_predicthaplo')"><span class=property-name>predicthaplo</span></button> </h2> </div> <div id=applications_predicthaplo class="collapse property-definition-div" aria-labelledby=headingapplications_predicthaplo data-parent=#accordionapplications_predicthaplo> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_predicthaplo onclick="anchorLink('applications_predicthaplo')">predicthaplo</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "predicthaplo"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_cojac> <div class=card> <div class=card-header id=headingapplications_cojac> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_cojac aria-expanded aria-controls=applications_cojac onclick="setAnchor('#applications_cojac')"><span class=property-name>cojac</span></button> </h2> </div> <div id=applications_cojac class="collapse property-definition-div" aria-labelledby=headingapplications_cojac data-parent=#accordionapplications_cojac> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_cojac onclick="anchorLink('applications_cojac')">cojac</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "cojac"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionapplications_lollipop> <div class=card> <div class=card-header id=headingapplications_lollipop> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#applications_lollipop aria-expanded aria-controls=applications_lollipop onclick="setAnchor('#applications_lollipop')"><span class=property-name>lollipop</span></button> </h2> </div> <div id=applications_lollipop class="collapse property-definition-div" aria-labelledby=headingapplications_lollipop data-parent=#accordionapplications_lollipop> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications onclick="anchorLink('applications')">applications</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#applications_lollipop onclick="anchorLink('applications_lollipop')">lollipop</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "lollipop"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordiongunzip> <div class=card> <div class=card-header id=headinggunzip> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#gunzip aria-expanded aria-controls=gunzip onclick="setAnchor('#gunzip')"><span class=property-name>gunzip</span></button> </h2> </div> <div id=gunzip class="collapse property-definition-div" aria-labelledby=headinggunzip data-parent=#accordiongunzip> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#gunzip onclick="anchorLink('gunzip')">gunzip</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordiongunzip_mem> <div class=card> <div class=card-header id=headinggunzip_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#gunzip_mem aria-expanded aria-controls=gunzip_mem onclick="setAnchor('#gunzip_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=gunzip_mem class="collapse property-definition-div" aria-labelledby=headinggunzip_mem data-parent=#accordiongunzip_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#gunzip onclick="anchorLink('gunzip')">gunzip</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#gunzip_mem onclick="anchorLink('gunzip_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 32</span><br> </div> </div> </div> </div> <div class=accordion id=accordiongunzip_time> <div class=card> <div class=card-header id=headinggunzip_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#gunzip_time aria-expanded aria-controls=gunzip_time onclick="setAnchor('#gunzip_time')"><span class=property-name>time</span></button> </h2> </div> <div id=gunzip_time class="collapse property-definition-div" aria-labelledby=headinggunzip_time data-parent=#accordiongunzip_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#gunzip onclick="anchorLink('gunzip')">gunzip</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#gunzip_time onclick="anchorLink('gunzip_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 60</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionextract> <div class=card> <div class=card-header id=headingextract> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#extract aria-expanded aria-controls=extract onclick="setAnchor('#extract')"><span class=property-name>extract</span></button> </h2> </div> <div id=extract class="collapse property-definition-div" aria-labelledby=headingextract data-parent=#accordionextract> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#extract onclick="anchorLink('extract')">extract</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionextract_mem> <div class=card> <div class=card-header id=headingextract_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#extract_mem aria-expanded aria-controls=extract_mem onclick="setAnchor('#extract_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=extract_mem class="collapse property-definition-div" aria-labelledby=headingextract_mem data-parent=#accordionextract_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#extract onclick="anchorLink('extract')">extract</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#extract_mem onclick="anchorLink('extract_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 4096</span><br> </div> </div> </div> </div> <div class=accordion id=accordionextract_time> <div class=card> <div class=card-header id=headingextract_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#extract_time aria-expanded aria-controls=extract_time onclick="setAnchor('#extract_time')"><span class=property-name>time</span></button> </h2> </div> <div id=extract_time class="collapse property-definition-div" aria-labelledby=headingextract_time data-parent=#accordionextract_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#extract onclick="anchorLink('extract')">extract</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#extract_time onclick="anchorLink('extract_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 20</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionpreprocessing> <div class=card> <div class=card-header id=headingpreprocessing> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#preprocessing aria-expanded aria-controls=preprocessing onclick="setAnchor('#preprocessing')"><span class=property-name>preprocessing</span></button> </h2> </div> <div id=preprocessing class="collapse property-definition-div" aria-labelledby=headingpreprocessing data-parent=#accordionpreprocessing> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#preprocessing onclick="anchorLink('preprocessing')">preprocessing</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionpreprocessing_mem> <div class=card> <div class=card-header id=headingpreprocessing_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#preprocessing_mem aria-expanded aria-controls=preprocessing_mem onclick="setAnchor('#preprocessing_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=preprocessing_mem class="collapse property-definition-div" aria-labelledby=headingpreprocessing_mem data-parent=#accordionpreprocessing_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#preprocessing onclick="anchorLink('preprocessing')">preprocessing</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#preprocessing_mem onclick="anchorLink('preprocessing_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 2000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionpreprocessing_time> <div class=card> <div class=card-header id=headingpreprocessing_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#preprocessing_time aria-expanded aria-controls=preprocessing_time onclick="setAnchor('#preprocessing_time')"><span class=property-name>time</span></button> </h2> </div> <div id=preprocessing_time class="collapse property-definition-div" aria-labelledby=headingpreprocessing_time data-parent=#accordionpreprocessing_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#preprocessing onclick="anchorLink('preprocessing')">preprocessing</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#preprocessing_time onclick="anchorLink('preprocessing_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionpreprocessing_conda> <div class=card> <div class=card-header id=headingpreprocessing_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#preprocessing_conda aria-expanded aria-controls=preprocessing_conda onclick="setAnchor('#preprocessing_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=preprocessing_conda class="collapse property-definition-div" aria-labelledby=headingpreprocessing_conda data-parent=#accordionpreprocessing_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#preprocessing onclick="anchorLink('preprocessing')">preprocessing</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#preprocessing_conda onclick="anchorLink('preprocessing_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/preprocessing.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionpreprocessing_extra> <div class=card> <div class=card-header id=headingpreprocessing_extra> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#preprocessing_extra aria-expanded aria-controls=preprocessing_extra onclick="setAnchor('#preprocessing_extra')"><span class=property-name>extra</span></button> </h2> </div> <div id=preprocessing_extra class="collapse property-definition-div" aria-labelledby=headingpreprocessing_extra data-parent=#accordionpreprocessing_extra> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#preprocessing onclick="anchorLink('preprocessing')">preprocessing</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#preprocessing_extra onclick="anchorLink('preprocessing_extra')">extra</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "-ns_max_n 4 -min_qual_mean 30 -trim_qual_left 30 -trim_qual_right 30 -trim_qual_window 10"</span><br> <span class=description><p>We use software PRINSEQ <sup class=footnote-ref id=fnref-10><a href=#fn-10>1</a></sup> for quality control. By default, we use options <code>-ns_max_n 4 -min_qual_mean 30 -trim_qual_left 30 -trim_qual_right 30 -trim_qual_window 10</code>, which indicates to trim reads using a sliding window with size 10 bp, and trim bases if their quality scores are less than 30. Additionally, reads are filtered out if the average quality score is below 30 and if they contain more than 4 N’s. The user can choose to overwrite the default settings or use additional parameters by using the property <code>extra</code>. E.g., if many reads are filtered out in this step, the user can choose to lower the quality threshold as indicated in the example.<br> Please do not modify PRINSEQ options <code>-out_format</code>, <code>-out_good</code>, nor <code>-min_len</code>. Instead of using <code>-min_len</code> to define threshold on the read length after trimming, use <a href=#input_trim_percent_cutoff><code>input</code> => <code>trim_percent_cutoff</code></a>.</p> <div class=footnotes> <hr> <ol> <li id=fn-10> <p>Schmieder, R. and Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011. <a href=#fnref-10 class=footnoteBackLink title="Jump back to footnote 1 in the text.">↩</a></p> </li> </ol> </div> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=preprocessing_extra_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">-ns_max_n 4 -min_qual_mean 20 -trim_qual_left 20 -trim_qual_right 20 -trim_qual_window 10</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionfastqc> <div class=card> <div class=card-header id=headingfastqc> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#fastqc aria-expanded aria-controls=fastqc onclick="setAnchor('#fastqc')"><span class=property-name>fastqc</span></button> </h2> </div> <div id=fastqc class="collapse property-definition-div" aria-labelledby=headingfastqc data-parent=#accordionfastqc> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#fastqc onclick="anchorLink('fastqc')">fastqc</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionfastqc_mem> <div class=card> <div class=card-header id=headingfastqc_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#fastqc_mem aria-expanded aria-controls=fastqc_mem onclick="setAnchor('#fastqc_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=fastqc_mem class="collapse property-definition-div" aria-labelledby=headingfastqc_mem data-parent=#accordionfastqc_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#fastqc onclick="anchorLink('fastqc')">fastqc</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#fastqc_mem onclick="anchorLink('fastqc_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 2000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionfastqc_time> <div class=card> <div class=card-header id=headingfastqc_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#fastqc_time aria-expanded aria-controls=fastqc_time onclick="setAnchor('#fastqc_time')"><span class=property-name>time</span></button> </h2> </div> <div id=fastqc_time class="collapse property-definition-div" aria-labelledby=headingfastqc_time data-parent=#accordionfastqc_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#fastqc onclick="anchorLink('fastqc')">fastqc</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#fastqc_time onclick="anchorLink('fastqc_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionfastqc_conda> <div class=card> <div class=card-header id=headingfastqc_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#fastqc_conda aria-expanded aria-controls=fastqc_conda onclick="setAnchor('#fastqc_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=fastqc_conda class="collapse property-definition-div" aria-labelledby=headingfastqc_conda data-parent=#accordionfastqc_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#fastqc onclick="anchorLink('fastqc')">fastqc</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#fastqc_conda onclick="anchorLink('fastqc_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/fastqc.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionfastqc_threads> <div class=card> <div class=card-header id=headingfastqc_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#fastqc_threads aria-expanded aria-controls=fastqc_threads onclick="setAnchor('#fastqc_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=fastqc_threads class="collapse property-definition-div" aria-labelledby=headingfastqc_threads data-parent=#accordionfastqc_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#fastqc onclick="anchorLink('fastqc')">fastqc</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#fastqc_threads onclick="anchorLink('fastqc_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 6</span><br> </div> </div> </div> </div> <div class=accordion id=accordionfastqc_no_group> <div class=card> <div class=card-header id=headingfastqc_no_group> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#fastqc_no_group aria-expanded aria-controls=fastqc_no_group onclick="setAnchor('#fastqc_no_group')"><span class=property-name>no_group</span></button> </h2> </div> <div id=fastqc_no_group class="collapse property-definition-div" aria-labelledby=headingfastqc_no_group data-parent=#accordionfastqc_no_group> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#fastqc onclick="anchorLink('fastqc')">fastqc</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#fastqc_no_group onclick="anchorLink('fastqc_no_group')">no_group</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninitial_vicuna> <div class=card> <div class=card-header id=headinginitial_vicuna> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#initial_vicuna aria-expanded aria-controls=initial_vicuna onclick="setAnchor('#initial_vicuna')"><span class=property-name>initial_vicuna</span></button> </h2> </div> <div id=initial_vicuna class="collapse property-definition-div" aria-labelledby=headinginitial_vicuna data-parent=#accordioninitial_vicuna> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna onclick="anchorLink('initial_vicuna')">initial_vicuna</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <span class=description><p><strong>NOTE</strong> The conda environment for this rule doesn’t work properly. The package on the bioconda channel, mvicuna, is slightly different from VICUNA and it has different command-line arguments. Moreover, VICUNA and mvicuna are no longer maintained. In the future, this rule will be deprecated.</p> </span> <div class=accordion id=accordioninitial_vicuna_mem> <div class=card> <div class=card-header id=headinginitial_vicuna_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#initial_vicuna_mem aria-expanded aria-controls=initial_vicuna_mem onclick="setAnchor('#initial_vicuna_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=initial_vicuna_mem class="collapse property-definition-div" aria-labelledby=headinginitial_vicuna_mem data-parent=#accordioninitial_vicuna_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna onclick="anchorLink('initial_vicuna')">initial_vicuna</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna_mem onclick="anchorLink('initial_vicuna_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1000</span><br> </div> </div> </div> </div> <div class=accordion id=accordioninitial_vicuna_time> <div class=card> <div class=card-header id=headinginitial_vicuna_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#initial_vicuna_time aria-expanded aria-controls=initial_vicuna_time onclick="setAnchor('#initial_vicuna_time')"><span class=property-name>time</span></button> </h2> </div> <div id=initial_vicuna_time class="collapse property-definition-div" aria-labelledby=headinginitial_vicuna_time data-parent=#accordioninitial_vicuna_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna onclick="anchorLink('initial_vicuna')">initial_vicuna</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna_time onclick="anchorLink('initial_vicuna_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 600</span><br> </div> </div> </div> </div> <div class=accordion id=accordioninitial_vicuna_threads> <div class=card> <div class=card-header id=headinginitial_vicuna_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#initial_vicuna_threads aria-expanded aria-controls=initial_vicuna_threads onclick="setAnchor('#initial_vicuna_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=initial_vicuna_threads class="collapse property-definition-div" aria-labelledby=headinginitial_vicuna_threads data-parent=#accordioninitial_vicuna_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna onclick="anchorLink('initial_vicuna')">initial_vicuna</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna_threads onclick="anchorLink('initial_vicuna_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordioninitial_vicuna_conda> <div class=card> <div class=card-header id=headinginitial_vicuna_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#initial_vicuna_conda aria-expanded aria-controls=initial_vicuna_conda onclick="setAnchor('#initial_vicuna_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=initial_vicuna_conda class="collapse property-definition-div" aria-labelledby=headinginitial_vicuna_conda data-parent=#accordioninitial_vicuna_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna onclick="anchorLink('initial_vicuna')">initial_vicuna</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna_conda onclick="anchorLink('initial_vicuna_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/initial_vicuna.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordioninitial_vicuna_msa> <div class=card> <div class=card-header id=headinginitial_vicuna_msa> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#initial_vicuna_msa aria-expanded aria-controls=initial_vicuna_msa onclick="setAnchor('#initial_vicuna_msa')"><span class=property-name>initial_vicuna_msa</span></button> </h2> </div> <div id=initial_vicuna_msa class="collapse property-definition-div" aria-labelledby=headinginitial_vicuna_msa data-parent=#accordioninitial_vicuna_msa> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna_msa onclick="anchorLink('initial_vicuna_msa')">initial_vicuna_msa</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <span class=description><p><strong>NOTE</strong> Obtaining a initial reference <em>de novo</em> is implemented for more than one sample.</p> </span> <div class=accordion id=accordioninitial_vicuna_msa_mem> <div class=card> <div class=card-header id=headinginitial_vicuna_msa_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#initial_vicuna_msa_mem aria-expanded aria-controls=initial_vicuna_msa_mem onclick="setAnchor('#initial_vicuna_msa_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=initial_vicuna_msa_mem class="collapse property-definition-div" aria-labelledby=headinginitial_vicuna_msa_mem data-parent=#accordioninitial_vicuna_msa_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna_msa onclick="anchorLink('initial_vicuna_msa')">initial_vicuna_msa</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna_msa_mem onclick="anchorLink('initial_vicuna_msa_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 10000</span><br> </div> </div> </div> </div> <div class=accordion id=accordioninitial_vicuna_msa_time> <div class=card> <div class=card-header id=headinginitial_vicuna_msa_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#initial_vicuna_msa_time aria-expanded aria-controls=initial_vicuna_msa_time onclick="setAnchor('#initial_vicuna_msa_time')"><span class=property-name>time</span></button> </h2> </div> <div id=initial_vicuna_msa_time class="collapse property-definition-div" aria-labelledby=headinginitial_vicuna_msa_time data-parent=#accordioninitial_vicuna_msa_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna_msa onclick="anchorLink('initial_vicuna_msa')">initial_vicuna_msa</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna_msa_time onclick="anchorLink('initial_vicuna_msa_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordioninitial_vicuna_msa_threads> <div class=card> <div class=card-header id=headinginitial_vicuna_msa_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#initial_vicuna_msa_threads aria-expanded aria-controls=initial_vicuna_msa_threads onclick="setAnchor('#initial_vicuna_msa_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=initial_vicuna_msa_threads class="collapse property-definition-div" aria-labelledby=headinginitial_vicuna_msa_threads data-parent=#accordioninitial_vicuna_msa_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna_msa onclick="anchorLink('initial_vicuna_msa')">initial_vicuna_msa</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna_msa_threads onclick="anchorLink('initial_vicuna_msa_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordioninitial_vicuna_msa_conda> <div class=card> <div class=card-header id=headinginitial_vicuna_msa_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#initial_vicuna_msa_conda aria-expanded aria-controls=initial_vicuna_msa_conda onclick="setAnchor('#initial_vicuna_msa_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=initial_vicuna_msa_conda class="collapse property-definition-div" aria-labelledby=headinginitial_vicuna_msa_conda data-parent=#accordioninitial_vicuna_msa_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna_msa onclick="anchorLink('initial_vicuna_msa')">initial_vicuna_msa</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#initial_vicuna_msa_conda onclick="anchorLink('initial_vicuna_msa_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/initial_vicuna_msa.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordioncreate_vicuna_initial> <div class=card> <div class=card-header id=headingcreate_vicuna_initial> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#create_vicuna_initial aria-expanded aria-controls=create_vicuna_initial onclick="setAnchor('#create_vicuna_initial')"><span class=property-name>create_vicuna_initial</span></button> </h2> </div> <div id=create_vicuna_initial class="collapse property-definition-div" aria-labelledby=headingcreate_vicuna_initial data-parent=#accordioncreate_vicuna_initial> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#create_vicuna_initial onclick="anchorLink('create_vicuna_initial')">create_vicuna_initial</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordioncreate_vicuna_initial_conda> <div class=card> <div class=card-header id=headingcreate_vicuna_initial_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#create_vicuna_initial_conda aria-expanded aria-controls=create_vicuna_initial_conda onclick="setAnchor('#create_vicuna_initial_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=create_vicuna_initial_conda class="collapse property-definition-div" aria-labelledby=headingcreate_vicuna_initial_conda data-parent=#accordioncreate_vicuna_initial_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#create_vicuna_initial onclick="anchorLink('create_vicuna_initial')">create_vicuna_initial</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#create_vicuna_initial_conda onclick="anchorLink('create_vicuna_initial_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/smallgenomeutilities.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionhmm_align> <div class=card> <div class=card-header id=headinghmm_align> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#hmm_align aria-expanded aria-controls=hmm_align onclick="setAnchor('#hmm_align')"><span class=property-name>hmm_align</span></button> </h2> </div> <div id=hmm_align class="collapse property-definition-div" aria-labelledby=headinghmm_align data-parent=#accordionhmm_align> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#hmm_align onclick="anchorLink('hmm_align')">hmm_align</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionhmm_align_mem> <div class=card> <div class=card-header id=headinghmm_align_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#hmm_align_mem aria-expanded aria-controls=hmm_align_mem onclick="setAnchor('#hmm_align_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=hmm_align_mem class="collapse property-definition-div" aria-labelledby=headinghmm_align_mem data-parent=#accordionhmm_align_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#hmm_align onclick="anchorLink('hmm_align')">hmm_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#hmm_align_mem onclick="anchorLink('hmm_align_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1250</span><br> </div> </div> </div> </div> <div class=accordion id=accordionhmm_align_time> <div class=card> <div class=card-header id=headinghmm_align_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#hmm_align_time aria-expanded aria-controls=hmm_align_time onclick="setAnchor('#hmm_align_time')"><span class=property-name>time</span></button> </h2> </div> <div id=hmm_align_time class="collapse property-definition-div" aria-labelledby=headinghmm_align_time data-parent=#accordionhmm_align_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#hmm_align onclick="anchorLink('hmm_align')">hmm_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#hmm_align_time onclick="anchorLink('hmm_align_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1435</span><br> </div> </div> </div> </div> <div class=accordion id=accordionhmm_align_threads> <div class=card> <div class=card-header id=headinghmm_align_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#hmm_align_threads aria-expanded aria-controls=hmm_align_threads onclick="setAnchor('#hmm_align_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=hmm_align_threads class="collapse property-definition-div" aria-labelledby=headinghmm_align_threads data-parent=#accordionhmm_align_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#hmm_align onclick="anchorLink('hmm_align')">hmm_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#hmm_align_threads onclick="anchorLink('hmm_align_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionhmm_align_conda> <div class=card> <div class=card-header id=headinghmm_align_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#hmm_align_conda aria-expanded aria-controls=hmm_align_conda onclick="setAnchor('#hmm_align_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=hmm_align_conda class="collapse property-definition-div" aria-labelledby=headinghmm_align_conda data-parent=#accordionhmm_align_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#hmm_align onclick="anchorLink('hmm_align')">hmm_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#hmm_align_conda onclick="anchorLink('hmm_align_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/hmm_align.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionhmm_align_leave_msa_temp> <div class=card> <div class=card-header id=headinghmm_align_leave_msa_temp> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#hmm_align_leave_msa_temp aria-expanded aria-controls=hmm_align_leave_msa_temp onclick="setAnchor('#hmm_align_leave_msa_temp')"><span class=property-name>leave_msa_temp</span></button> </h2> </div> <div id=hmm_align_leave_msa_temp class="collapse property-definition-div" aria-labelledby=headinghmm_align_leave_msa_temp data-parent=#accordionhmm_align_leave_msa_temp> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#hmm_align onclick="anchorLink('hmm_align')">hmm_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#hmm_align_leave_msa_temp onclick="anchorLink('hmm_align_leave_msa_temp')">leave_msa_temp</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>This option is useful for debugging purposes.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=hmm_align_leave_msa_temp_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionhmm_align_extra> <div class=card> <div class=card-header id=headinghmm_align_extra> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#hmm_align_extra aria-expanded aria-controls=hmm_align_extra onclick="setAnchor('#hmm_align_extra')"><span class=property-name>extra</span></button> </h2> </div> <div id=hmm_align_extra class="collapse property-definition-div" aria-labelledby=headinghmm_align_extra data-parent=#accordionhmm_align_extra> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#hmm_align onclick="anchorLink('hmm_align')">hmm_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#hmm_align_extra onclick="anchorLink('hmm_align_extra')">extra</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>Pass additional options to run ngshmmalign</p> <p>V-pipe uses option <code>-R <path/to/initial_reference></code>, thus option <code>-r arg</code> is not allowed. Also, instead of passing <code>-l</code> via the property <code>extra</code>, set <a href=#hmm_align_leave_msa_temp><code>leave_msa_temp</code></a> to <code>True</code>. Lastly, please do not modify options <code>-o arg</code>, <code>-w arg</code>, <code>-t arg</code>, and <code>-N arg</code>. These are already managed by V-pipe.</p> </span> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionsam2bam> <div class=card> <div class=card-header id=headingsam2bam> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#sam2bam aria-expanded aria-controls=sam2bam onclick="setAnchor('#sam2bam')"><span class=property-name>sam2bam</span></button> </h2> </div> <div id=sam2bam class="collapse property-definition-div" aria-labelledby=headingsam2bam data-parent=#accordionsam2bam> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#sam2bam onclick="anchorLink('sam2bam')">sam2bam</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionsam2bam_mem> <div class=card> <div class=card-header id=headingsam2bam_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#sam2bam_mem aria-expanded aria-controls=sam2bam_mem onclick="setAnchor('#sam2bam_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=sam2bam_mem class="collapse property-definition-div" aria-labelledby=headingsam2bam_mem data-parent=#accordionsam2bam_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#sam2bam onclick="anchorLink('sam2bam')">sam2bam</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#sam2bam_mem onclick="anchorLink('sam2bam_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 5000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionsam2bam_time> <div class=card> <div class=card-header id=headingsam2bam_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#sam2bam_time aria-expanded aria-controls=sam2bam_time onclick="setAnchor('#sam2bam_time')"><span class=property-name>time</span></button> </h2> </div> <div id=sam2bam_time class="collapse property-definition-div" aria-labelledby=headingsam2bam_time data-parent=#accordionsam2bam_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#sam2bam onclick="anchorLink('sam2bam')">sam2bam</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#sam2bam_time onclick="anchorLink('sam2bam_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 30</span><br> </div> </div> </div> </div> <div class=accordion id=accordionsam2bam_conda> <div class=card> <div class=card-header id=headingsam2bam_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#sam2bam_conda aria-expanded aria-controls=sam2bam_conda onclick="setAnchor('#sam2bam_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=sam2bam_conda class="collapse property-definition-div" aria-labelledby=headingsam2bam_conda data-parent=#accordionsam2bam_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#sam2bam onclick="anchorLink('sam2bam')">sam2bam</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#sam2bam_conda onclick="anchorLink('sam2bam_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/sam2bam.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionbwa_QA> <div class=card> <div class=card-header id=headingbwa_QA> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bwa_QA aria-expanded aria-controls=bwa_QA onclick="setAnchor('#bwa_QA')"><span class=property-name>bwa_QA</span></button> </h2> </div> <div id=bwa_QA class="collapse property-definition-div" aria-labelledby=headingbwa_QA data-parent=#accordionbwa_QA> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_QA onclick="anchorLink('bwa_QA')">bwa_QA</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionbwa_QA_mem> <div class=card> <div class=card-header id=headingbwa_QA_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bwa_QA_mem aria-expanded aria-controls=bwa_QA_mem onclick="setAnchor('#bwa_QA_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=bwa_QA_mem class="collapse property-definition-div" aria-labelledby=headingbwa_QA_mem data-parent=#accordionbwa_QA_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_QA onclick="anchorLink('bwa_QA')">bwa_QA</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_QA_mem onclick="anchorLink('bwa_QA_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1250</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbwa_QA_time> <div class=card> <div class=card-header id=headingbwa_QA_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bwa_QA_time aria-expanded aria-controls=bwa_QA_time onclick="setAnchor('#bwa_QA_time')"><span class=property-name>time</span></button> </h2> </div> <div id=bwa_QA_time class="collapse property-definition-div" aria-labelledby=headingbwa_QA_time data-parent=#accordionbwa_QA_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_QA onclick="anchorLink('bwa_QA')">bwa_QA</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_QA_time onclick="anchorLink('bwa_QA_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbwa_QA_threads> <div class=card> <div class=card-header id=headingbwa_QA_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bwa_QA_threads aria-expanded aria-controls=bwa_QA_threads onclick="setAnchor('#bwa_QA_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=bwa_QA_threads class="collapse property-definition-div" aria-labelledby=headingbwa_QA_threads data-parent=#accordionbwa_QA_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_QA onclick="anchorLink('bwa_QA')">bwa_QA</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_QA_threads onclick="anchorLink('bwa_QA_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbwa_QA_conda> <div class=card> <div class=card-header id=headingbwa_QA_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bwa_QA_conda aria-expanded aria-controls=bwa_QA_conda onclick="setAnchor('#bwa_QA_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=bwa_QA_conda class="collapse property-definition-div" aria-labelledby=headingbwa_QA_conda data-parent=#accordionbwa_QA_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_QA onclick="anchorLink('bwa_QA')">bwa_QA</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_QA_conda onclick="anchorLink('bwa_QA_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/bwa_QA.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbwa_QA_ref_panel> <div class=card> <div class=card-header id=headingbwa_QA_ref_panel> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bwa_QA_ref_panel aria-expanded aria-controls=bwa_QA_ref_panel onclick="setAnchor('#bwa_QA_ref_panel')"><span class=property-name>ref_panel</span></button> </h2> </div> <div id=bwa_QA_ref_panel class="collapse property-definition-div" aria-labelledby=headingbwa_QA_ref_panel data-parent=#accordionbwa_QA_ref_panel> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_QA onclick="anchorLink('bwa_QA')">bwa_QA</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_QA_ref_panel onclick="anchorLink('bwa_QA_ref_panel')">ref_panel</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>Panel of diverse references against which to align reads as a QA step</p> <p><strong>Note</strong>: The virus-specific base configuration specified in <a href=#general_virus_base_config><code>general</code> => <code>virus_base_config</code></a> will most likely change this option’s default.<br> You are still free to override that default in your configuration shall the need arise.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=bwa_QA_ref_panel_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">resources/hiv/5-Virus-Mix.fasta</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_QA> <div class=card> <div class=card-header id=headingcoverage_QA> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_QA aria-expanded aria-controls=coverage_QA onclick="setAnchor('#coverage_QA')"><span class=property-name>coverage_QA</span></button> </h2> </div> <div id=coverage_QA class="collapse property-definition-div" aria-labelledby=headingcoverage_QA data-parent=#accordioncoverage_QA> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_QA onclick="anchorLink('coverage_QA')">coverage_QA</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordioncoverage_QA_mem> <div class=card> <div class=card-header id=headingcoverage_QA_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_QA_mem aria-expanded aria-controls=coverage_QA_mem onclick="setAnchor('#coverage_QA_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=coverage_QA_mem class="collapse property-definition-div" aria-labelledby=headingcoverage_QA_mem data-parent=#accordioncoverage_QA_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_QA onclick="anchorLink('coverage_QA')">coverage_QA</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_QA_mem onclick="anchorLink('coverage_QA_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1250</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_QA_time> <div class=card> <div class=card-header id=headingcoverage_QA_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_QA_time aria-expanded aria-controls=coverage_QA_time onclick="setAnchor('#coverage_QA_time')"><span class=property-name>time</span></button> </h2> </div> <div id=coverage_QA_time class="collapse property-definition-div" aria-labelledby=headingcoverage_QA_time data-parent=#accordioncoverage_QA_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_QA onclick="anchorLink('coverage_QA')">coverage_QA</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_QA_time onclick="anchorLink('coverage_QA_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_QA_conda> <div class=card> <div class=card-header id=headingcoverage_QA_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_QA_conda aria-expanded aria-controls=coverage_QA_conda onclick="setAnchor('#coverage_QA_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=coverage_QA_conda class="collapse property-definition-div" aria-labelledby=headingcoverage_QA_conda data-parent=#accordioncoverage_QA_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_QA onclick="anchorLink('coverage_QA')">coverage_QA</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_QA_conda onclick="anchorLink('coverage_QA_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/smallgenomeutilities.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_QA_target> <div class=card> <div class=card-header id=headingcoverage_QA_target> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_QA_target aria-expanded aria-controls=coverage_QA_target onclick="setAnchor('#coverage_QA_target')"><span class=property-name>target</span></button> </h2> </div> <div id=coverage_QA_target class="collapse property-definition-div" aria-labelledby=headingcoverage_QA_target data-parent=#accordioncoverage_QA_target> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_QA onclick="anchorLink('coverage_QA')">coverage_QA</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_QA_target onclick="anchorLink('coverage_QA_target')">target</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "HXB2:6614-6812,7109-7217,7376-7478,7601-7634"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionmsa> <div class=card> <div class=card-header id=headingmsa> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#msa aria-expanded aria-controls=msa onclick="setAnchor('#msa')"><span class=property-name>msa</span></button> </h2> </div> <div id=msa class="collapse property-definition-div" aria-labelledby=headingmsa data-parent=#accordionmsa> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#msa onclick="anchorLink('msa')">msa</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <span class=description><p>This rule takes all previously aligned reads by <code>hmm_align</code>. Therefore, resources should be allocated accordingly.</p> </span> <div class=accordion id=accordionmsa_mem> <div class=card> <div class=card-header id=headingmsa_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#msa_mem aria-expanded aria-controls=msa_mem onclick="setAnchor('#msa_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=msa_mem class="collapse property-definition-div" aria-labelledby=headingmsa_mem data-parent=#accordionmsa_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#msa onclick="anchorLink('msa')">msa</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#msa_mem onclick="anchorLink('msa_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 10000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionmsa_time> <div class=card> <div class=card-header id=headingmsa_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#msa_time aria-expanded aria-controls=msa_time onclick="setAnchor('#msa_time')"><span class=property-name>time</span></button> </h2> </div> <div id=msa_time class="collapse property-definition-div" aria-labelledby=headingmsa_time data-parent=#accordionmsa_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#msa onclick="anchorLink('msa')">msa</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#msa_time onclick="anchorLink('msa_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionmsa_threads> <div class=card> <div class=card-header id=headingmsa_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#msa_threads aria-expanded aria-controls=msa_threads onclick="setAnchor('#msa_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=msa_threads class="collapse property-definition-div" aria-labelledby=headingmsa_threads data-parent=#accordionmsa_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#msa onclick="anchorLink('msa')">msa</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#msa_threads onclick="anchorLink('msa_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionmsa_conda> <div class=card> <div class=card-header id=headingmsa_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#msa_conda aria-expanded aria-controls=msa_conda onclick="setAnchor('#msa_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=msa_conda class="collapse property-definition-div" aria-labelledby=headingmsa_conda data-parent=#accordionmsa_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#msa onclick="anchorLink('msa')">msa</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#msa_conda onclick="anchorLink('msa_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/msa.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionconvert_to_ref> <div class=card> <div class=card-header id=headingconvert_to_ref> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#convert_to_ref aria-expanded aria-controls=convert_to_ref onclick="setAnchor('#convert_to_ref')"><span class=property-name>convert_to_ref</span></button> </h2> </div> <div id=convert_to_ref class="collapse property-definition-div" aria-labelledby=headingconvert_to_ref data-parent=#accordionconvert_to_ref> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#convert_to_ref onclick="anchorLink('convert_to_ref')">convert_to_ref</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionconvert_to_ref_mem> <div class=card> <div class=card-header id=headingconvert_to_ref_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#convert_to_ref_mem aria-expanded aria-controls=convert_to_ref_mem onclick="setAnchor('#convert_to_ref_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=convert_to_ref_mem class="collapse property-definition-div" aria-labelledby=headingconvert_to_ref_mem data-parent=#accordionconvert_to_ref_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#convert_to_ref onclick="anchorLink('convert_to_ref')">convert_to_ref</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#convert_to_ref_mem onclick="anchorLink('convert_to_ref_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 8000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconvert_to_ref_time> <div class=card> <div class=card-header id=headingconvert_to_ref_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#convert_to_ref_time aria-expanded aria-controls=convert_to_ref_time onclick="setAnchor('#convert_to_ref_time')"><span class=property-name>time</span></button> </h2> </div> <div id=convert_to_ref_time class="collapse property-definition-div" aria-labelledby=headingconvert_to_ref_time data-parent=#accordionconvert_to_ref_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#convert_to_ref onclick="anchorLink('convert_to_ref')">convert_to_ref</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#convert_to_ref_time onclick="anchorLink('convert_to_ref_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconvert_to_ref_conda> <div class=card> <div class=card-header id=headingconvert_to_ref_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#convert_to_ref_conda aria-expanded aria-controls=convert_to_ref_conda onclick="setAnchor('#convert_to_ref_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=convert_to_ref_conda class="collapse property-definition-div" aria-labelledby=headingconvert_to_ref_conda data-parent=#accordionconvert_to_ref_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#convert_to_ref onclick="anchorLink('convert_to_ref')">convert_to_ref</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#convert_to_ref_conda onclick="anchorLink('convert_to_ref_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/smallgenomeutilities.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionref_bwa_index> <div class=card> <div class=card-header id=headingref_bwa_index> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#ref_bwa_index aria-expanded aria-controls=ref_bwa_index onclick="setAnchor('#ref_bwa_index')"><span class=property-name>ref_bwa_index</span></button> </h2> </div> <div id=ref_bwa_index class="collapse property-definition-div" aria-labelledby=headingref_bwa_index data-parent=#accordionref_bwa_index> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bwa_index onclick="anchorLink('ref_bwa_index')">ref_bwa_index</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionref_bwa_index_mem> <div class=card> <div class=card-header id=headingref_bwa_index_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#ref_bwa_index_mem aria-expanded aria-controls=ref_bwa_index_mem onclick="setAnchor('#ref_bwa_index_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=ref_bwa_index_mem class="collapse property-definition-div" aria-labelledby=headingref_bwa_index_mem data-parent=#accordionref_bwa_index_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bwa_index onclick="anchorLink('ref_bwa_index')">ref_bwa_index</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bwa_index_mem onclick="anchorLink('ref_bwa_index_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 2000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionref_bwa_index_time> <div class=card> <div class=card-header id=headingref_bwa_index_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#ref_bwa_index_time aria-expanded aria-controls=ref_bwa_index_time onclick="setAnchor('#ref_bwa_index_time')"><span class=property-name>time</span></button> </h2> </div> <div id=ref_bwa_index_time class="collapse property-definition-div" aria-labelledby=headingref_bwa_index_time data-parent=#accordionref_bwa_index_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bwa_index onclick="anchorLink('ref_bwa_index')">ref_bwa_index</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bwa_index_time onclick="anchorLink('ref_bwa_index_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionref_bwa_index_conda> <div class=card> <div class=card-header id=headingref_bwa_index_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#ref_bwa_index_conda aria-expanded aria-controls=ref_bwa_index_conda onclick="setAnchor('#ref_bwa_index_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=ref_bwa_index_conda class="collapse property-definition-div" aria-labelledby=headingref_bwa_index_conda data-parent=#accordionref_bwa_index_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bwa_index onclick="anchorLink('ref_bwa_index')">ref_bwa_index</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bwa_index_conda onclick="anchorLink('ref_bwa_index_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/bwa_align.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionbwa_align> <div class=card> <div class=card-header id=headingbwa_align> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bwa_align aria-expanded aria-controls=bwa_align onclick="setAnchor('#bwa_align')"><span class=property-name>bwa_align</span></button> </h2> </div> <div id=bwa_align class="collapse property-definition-div" aria-labelledby=headingbwa_align data-parent=#accordionbwa_align> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_align onclick="anchorLink('bwa_align')">bwa_align</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionbwa_align_mem> <div class=card> <div class=card-header id=headingbwa_align_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bwa_align_mem aria-expanded aria-controls=bwa_align_mem onclick="setAnchor('#bwa_align_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=bwa_align_mem class="collapse property-definition-div" aria-labelledby=headingbwa_align_mem data-parent=#accordionbwa_align_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_align onclick="anchorLink('bwa_align')">bwa_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_align_mem onclick="anchorLink('bwa_align_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1250</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbwa_align_time> <div class=card> <div class=card-header id=headingbwa_align_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bwa_align_time aria-expanded aria-controls=bwa_align_time onclick="setAnchor('#bwa_align_time')"><span class=property-name>time</span></button> </h2> </div> <div id=bwa_align_time class="collapse property-definition-div" aria-labelledby=headingbwa_align_time data-parent=#accordionbwa_align_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_align onclick="anchorLink('bwa_align')">bwa_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_align_time onclick="anchorLink('bwa_align_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbwa_align_threads> <div class=card> <div class=card-header id=headingbwa_align_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bwa_align_threads aria-expanded aria-controls=bwa_align_threads onclick="setAnchor('#bwa_align_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=bwa_align_threads class="collapse property-definition-div" aria-labelledby=headingbwa_align_threads data-parent=#accordionbwa_align_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_align onclick="anchorLink('bwa_align')">bwa_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_align_threads onclick="anchorLink('bwa_align_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbwa_align_conda> <div class=card> <div class=card-header id=headingbwa_align_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bwa_align_conda aria-expanded aria-controls=bwa_align_conda onclick="setAnchor('#bwa_align_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=bwa_align_conda class="collapse property-definition-div" aria-labelledby=headingbwa_align_conda data-parent=#accordionbwa_align_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_align onclick="anchorLink('bwa_align')">bwa_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_align_conda onclick="anchorLink('bwa_align_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/bwa_align.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbwa_align_extra> <div class=card> <div class=card-header id=headingbwa_align_extra> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bwa_align_extra aria-expanded aria-controls=bwa_align_extra onclick="setAnchor('#bwa_align_extra')"><span class=property-name>extra</span></button> </h2> </div> <div id=bwa_align_extra class="collapse property-definition-div" aria-labelledby=headingbwa_align_extra data-parent=#accordionbwa_align_extra> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_align onclick="anchorLink('bwa_align')">bwa_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bwa_align_extra onclick="anchorLink('bwa_align_extra')">extra</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>With property <code>extra</code>, users can pass additional options to run BWA MEM. For more details on BWA MEM configurable options refer to the software <a href=http://bio-bwa.sourceforge.net/bwa.shtml>documentation</a>.</p> </span> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionref_bowtie_index> <div class=card> <div class=card-header id=headingref_bowtie_index> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#ref_bowtie_index aria-expanded aria-controls=ref_bowtie_index onclick="setAnchor('#ref_bowtie_index')"><span class=property-name>ref_bowtie_index</span></button> </h2> </div> <div id=ref_bowtie_index class="collapse property-definition-div" aria-labelledby=headingref_bowtie_index data-parent=#accordionref_bowtie_index> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bowtie_index onclick="anchorLink('ref_bowtie_index')">ref_bowtie_index</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionref_bowtie_index_mem> <div class=card> <div class=card-header id=headingref_bowtie_index_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#ref_bowtie_index_mem aria-expanded aria-controls=ref_bowtie_index_mem onclick="setAnchor('#ref_bowtie_index_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=ref_bowtie_index_mem class="collapse property-definition-div" aria-labelledby=headingref_bowtie_index_mem data-parent=#accordionref_bowtie_index_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bowtie_index onclick="anchorLink('ref_bowtie_index')">ref_bowtie_index</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bowtie_index_mem onclick="anchorLink('ref_bowtie_index_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 2000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionref_bowtie_index_time> <div class=card> <div class=card-header id=headingref_bowtie_index_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#ref_bowtie_index_time aria-expanded aria-controls=ref_bowtie_index_time onclick="setAnchor('#ref_bowtie_index_time')"><span class=property-name>time</span></button> </h2> </div> <div id=ref_bowtie_index_time class="collapse property-definition-div" aria-labelledby=headingref_bowtie_index_time data-parent=#accordionref_bowtie_index_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bowtie_index onclick="anchorLink('ref_bowtie_index')">ref_bowtie_index</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bowtie_index_time onclick="anchorLink('ref_bowtie_index_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionref_bowtie_index_conda> <div class=card> <div class=card-header id=headingref_bowtie_index_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#ref_bowtie_index_conda aria-expanded aria-controls=ref_bowtie_index_conda onclick="setAnchor('#ref_bowtie_index_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=ref_bowtie_index_conda class="collapse property-definition-div" aria-labelledby=headingref_bowtie_index_conda data-parent=#accordionref_bowtie_index_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bowtie_index onclick="anchorLink('ref_bowtie_index')">ref_bowtie_index</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_bowtie_index_conda onclick="anchorLink('ref_bowtie_index_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/bowtie_align.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionbowtie_align> <div class=card> <div class=card-header id=headingbowtie_align> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bowtie_align aria-expanded aria-controls=bowtie_align onclick="setAnchor('#bowtie_align')"><span class=property-name>bowtie_align</span></button> </h2> </div> <div id=bowtie_align class="collapse property-definition-div" aria-labelledby=headingbowtie_align data-parent=#accordionbowtie_align> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align onclick="anchorLink('bowtie_align')">bowtie_align</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionbowtie_align_mem> <div class=card> <div class=card-header id=headingbowtie_align_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bowtie_align_mem aria-expanded aria-controls=bowtie_align_mem onclick="setAnchor('#bowtie_align_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=bowtie_align_mem class="collapse property-definition-div" aria-labelledby=headingbowtie_align_mem data-parent=#accordionbowtie_align_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align onclick="anchorLink('bowtie_align')">bowtie_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align_mem onclick="anchorLink('bowtie_align_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1250</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbowtie_align_time> <div class=card> <div class=card-header id=headingbowtie_align_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bowtie_align_time aria-expanded aria-controls=bowtie_align_time onclick="setAnchor('#bowtie_align_time')"><span class=property-name>time</span></button> </h2> </div> <div id=bowtie_align_time class="collapse property-definition-div" aria-labelledby=headingbowtie_align_time data-parent=#accordionbowtie_align_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align onclick="anchorLink('bowtie_align')">bowtie_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align_time onclick="anchorLink('bowtie_align_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbowtie_align_threads> <div class=card> <div class=card-header id=headingbowtie_align_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bowtie_align_threads aria-expanded aria-controls=bowtie_align_threads onclick="setAnchor('#bowtie_align_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=bowtie_align_threads class="collapse property-definition-div" aria-labelledby=headingbowtie_align_threads data-parent=#accordionbowtie_align_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align onclick="anchorLink('bowtie_align')">bowtie_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align_threads onclick="anchorLink('bowtie_align_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbowtie_align_conda> <div class=card> <div class=card-header id=headingbowtie_align_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bowtie_align_conda aria-expanded aria-controls=bowtie_align_conda onclick="setAnchor('#bowtie_align_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=bowtie_align_conda class="collapse property-definition-div" aria-labelledby=headingbowtie_align_conda data-parent=#accordionbowtie_align_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align onclick="anchorLink('bowtie_align')">bowtie_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align_conda onclick="anchorLink('bowtie_align_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/bowtie_align.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbowtie_align_phred> <div class=card> <div class=card-header id=headingbowtie_align_phred> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bowtie_align_phred aria-expanded aria-controls=bowtie_align_phred onclick="setAnchor('#bowtie_align_phred')"><span class=property-name>phred</span></button> </h2> </div> <div id=bowtie_align_phred class="collapse property-definition-div" aria-labelledby=headingbowtie_align_phred data-parent=#accordionbowtie_align_phred> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align onclick="anchorLink('bowtie_align')">bowtie_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align_phred onclick="anchorLink('bowtie_align_phred')">phred</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "--phred33"</span><br> <span class=description><p>Indicate if qualities are Phred+33 (default) or Phred+64 (<code>--phred64</code>).</p> </span><div class=enum-value id=bowtie_align_phred_enum> <h4>Must be one of:</h4> <ul class=list-group><li class="list-group-item enum-item">"--phred33"</li><li class="list-group-item enum-item">"--phred64"</li></ul> </div> <br> <div class="badge badge-secondary">Example:</div> <br><div id=bowtie_align_phred_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">--phred64</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionbowtie_align_preset> <div class=card> <div class=card-header id=headingbowtie_align_preset> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bowtie_align_preset aria-expanded aria-controls=bowtie_align_preset onclick="setAnchor('#bowtie_align_preset')"><span class=property-name>preset</span></button> </h2> </div> <div id=bowtie_align_preset class="collapse property-definition-div" aria-labelledby=headingbowtie_align_preset data-parent=#accordionbowtie_align_preset> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align onclick="anchorLink('bowtie_align')">bowtie_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align_preset onclick="anchorLink('bowtie_align_preset')">preset</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "--local --sensitive-local"</span><br> <span class=description><p>Specify Bowtie 2 presets.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionbowtie_align_maxins> <div class=card> <div class=card-header id=headingbowtie_align_maxins> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bowtie_align_maxins aria-expanded aria-controls=bowtie_align_maxins onclick="setAnchor('#bowtie_align_maxins')"><span class=property-name>maxins</span></button> </h2> </div> <div id=bowtie_align_maxins class="collapse property-definition-div" aria-labelledby=headingbowtie_align_maxins data-parent=#accordionbowtie_align_maxins> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align onclick="anchorLink('bowtie_align')">bowtie_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align_maxins onclick="anchorLink('bowtie_align_maxins')">maxins</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbowtie_align_extra> <div class=card> <div class=card-header id=headingbowtie_align_extra> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#bowtie_align_extra aria-expanded aria-controls=bowtie_align_extra onclick="setAnchor('#bowtie_align_extra')"><span class=property-name>extra</span></button> </h2> </div> <div id=bowtie_align_extra class="collapse property-definition-div" aria-labelledby=headingbowtie_align_extra data-parent=#accordionbowtie_align_extra> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align onclick="anchorLink('bowtie_align')">bowtie_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#bowtie_align_extra onclick="anchorLink('bowtie_align_extra')">extra</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>Pass additional options to run Bowtie 2. V-pipe handles the input and output files, as well as the reference sequence. Thus, do not modify these options<br> For more details on Bowtie 2 configurable options refer to the software <a href=http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml>documentation</a>.</p> </span> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionref_minimap_index> <div class=card> <div class=card-header id=headingref_minimap_index> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#ref_minimap_index aria-expanded aria-controls=ref_minimap_index onclick="setAnchor('#ref_minimap_index')"><span class=property-name>ref_minimap_index</span></button> </h2> </div> <div id=ref_minimap_index class="collapse property-definition-div" aria-labelledby=headingref_minimap_index data-parent=#accordionref_minimap_index> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_minimap_index onclick="anchorLink('ref_minimap_index')">ref_minimap_index</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionref_minimap_index_mem> <div class=card> <div class=card-header id=headingref_minimap_index_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#ref_minimap_index_mem aria-expanded aria-controls=ref_minimap_index_mem onclick="setAnchor('#ref_minimap_index_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=ref_minimap_index_mem class="collapse property-definition-div" aria-labelledby=headingref_minimap_index_mem data-parent=#accordionref_minimap_index_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_minimap_index onclick="anchorLink('ref_minimap_index')">ref_minimap_index</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_minimap_index_mem onclick="anchorLink('ref_minimap_index_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 2000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionref_minimap_index_time> <div class=card> <div class=card-header id=headingref_minimap_index_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#ref_minimap_index_time aria-expanded aria-controls=ref_minimap_index_time onclick="setAnchor('#ref_minimap_index_time')"><span class=property-name>time</span></button> </h2> </div> <div id=ref_minimap_index_time class="collapse property-definition-div" aria-labelledby=headingref_minimap_index_time data-parent=#accordionref_minimap_index_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_minimap_index onclick="anchorLink('ref_minimap_index')">ref_minimap_index</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_minimap_index_time onclick="anchorLink('ref_minimap_index_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionref_minimap_index_conda> <div class=card> <div class=card-header id=headingref_minimap_index_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#ref_minimap_index_conda aria-expanded aria-controls=ref_minimap_index_conda onclick="setAnchor('#ref_minimap_index_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=ref_minimap_index_conda class="collapse property-definition-div" aria-labelledby=headingref_minimap_index_conda data-parent=#accordionref_minimap_index_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_minimap_index onclick="anchorLink('ref_minimap_index')">ref_minimap_index</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#ref_minimap_index_conda onclick="anchorLink('ref_minimap_index_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/minimap_align.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionminimap_align> <div class=card> <div class=card-header id=headingminimap_align> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minimap_align aria-expanded aria-controls=minimap_align onclick="setAnchor('#minimap_align')"><span class=property-name>minimap_align</span></button> </h2> </div> <div id=minimap_align class="collapse property-definition-div" aria-labelledby=headingminimap_align data-parent=#accordionminimap_align> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align onclick="anchorLink('minimap_align')">minimap_align</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionminimap_align_mem> <div class=card> <div class=card-header id=headingminimap_align_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minimap_align_mem aria-expanded aria-controls=minimap_align_mem onclick="setAnchor('#minimap_align_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=minimap_align_mem class="collapse property-definition-div" aria-labelledby=headingminimap_align_mem data-parent=#accordionminimap_align_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align onclick="anchorLink('minimap_align')">minimap_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align_mem onclick="anchorLink('minimap_align_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1250</span><br> </div> </div> </div> </div> <div class=accordion id=accordionminimap_align_time> <div class=card> <div class=card-header id=headingminimap_align_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minimap_align_time aria-expanded aria-controls=minimap_align_time onclick="setAnchor('#minimap_align_time')"><span class=property-name>time</span></button> </h2> </div> <div id=minimap_align_time class="collapse property-definition-div" aria-labelledby=headingminimap_align_time data-parent=#accordionminimap_align_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align onclick="anchorLink('minimap_align')">minimap_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align_time onclick="anchorLink('minimap_align_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionminimap_align_threads> <div class=card> <div class=card-header id=headingminimap_align_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minimap_align_threads aria-expanded aria-controls=minimap_align_threads onclick="setAnchor('#minimap_align_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=minimap_align_threads class="collapse property-definition-div" aria-labelledby=headingminimap_align_threads data-parent=#accordionminimap_align_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align onclick="anchorLink('minimap_align')">minimap_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align_threads onclick="anchorLink('minimap_align_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionminimap_align_preset> <div class=card> <div class=card-header id=headingminimap_align_preset> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minimap_align_preset aria-expanded aria-controls=minimap_align_preset onclick="setAnchor('#minimap_align_preset')"><span class=property-name>preset</span></button> </h2> </div> <div id=minimap_align_preset class="collapse property-definition-div" aria-labelledby=headingminimap_align_preset data-parent=#accordionminimap_align_preset> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align onclick="anchorLink('minimap_align')">minimap_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align_preset onclick="anchorLink('minimap_align_preset')">preset</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "sr"</span><br> <span class=description><p>Specify minimap2 preset options. See <a href=https://lh3.github.io/minimap2/minimap2.html#8>minimape’s documentation</a> for details about each of the presets.</p> </span><div class=enum-value id=minimap_align_preset_enum> <h4>Must be one of:</h4> <ul class=list-group><li class="list-group-item enum-item">"map-ont"</li><li class="list-group-item enum-item">"map-hifi"</li><li class="list-group-item enum-item">"map-pb"</li><li class="list-group-item enum-item">"asm5"</li><li class="list-group-item enum-item">"asm10"</li><li class="list-group-item enum-item">"asm20"</li><li class="list-group-item enum-item">"splice"</li><li class="list-group-item enum-item">"splice:hq"</li><li class="list-group-item enum-item">"sr"</li><li class="list-group-item enum-item">"ava-pb"</li><li class="list-group-item enum-item">"ava-ont"</li></ul> </div> <br> <div class="badge badge-secondary">Example:</div> <br><div id=minimap_align_preset_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">map-ont</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionminimap_align_secondary> <div class=card> <div class=card-header id=headingminimap_align_secondary> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minimap_align_secondary aria-expanded aria-controls=minimap_align_secondary onclick="setAnchor('#minimap_align_secondary')"><span class=property-name>secondary</span></button> </h2> </div> <div id=minimap_align_secondary class="collapse property-definition-div" aria-labelledby=headingminimap_align_secondary data-parent=#accordionminimap_align_secondary> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align onclick="anchorLink('minimap_align')">minimap_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align_secondary onclick="anchorLink('minimap_align_secondary')">secondary</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>By default V-pipe ignores Minimap2’s secondary alignment(s) and only considers the primary one (A secondary alignment occurs when a given read could align reasonably well to more than one place). This flags turns back on Minimap2’s secondary alignments, and also includes their sequences in the output BAM file.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=minimap_align_secondary_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionminimap_align_conda> <div class=card> <div class=card-header id=headingminimap_align_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minimap_align_conda aria-expanded aria-controls=minimap_align_conda onclick="setAnchor('#minimap_align_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=minimap_align_conda class="collapse property-definition-div" aria-labelledby=headingminimap_align_conda data-parent=#accordionminimap_align_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align onclick="anchorLink('minimap_align')">minimap_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align_conda onclick="anchorLink('minimap_align_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/minimap_align.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionminimap_align_extra> <div class=card> <div class=card-header id=headingminimap_align_extra> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minimap_align_extra aria-expanded aria-controls=minimap_align_extra onclick="setAnchor('#minimap_align_extra')"><span class=property-name>extra</span></button> </h2> </div> <div id=minimap_align_extra class="collapse property-definition-div" aria-labelledby=headingminimap_align_extra data-parent=#accordionminimap_align_extra> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align onclick="anchorLink('minimap_align')">minimap_align</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minimap_align_extra onclick="anchorLink('minimap_align_extra')">extra</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>With property <code>extra</code>, users can pass additional options to run minimap2. For more details on minimap2 configurable options refer to the software <a href=https://github.com/lh3/minimap2>documentation</a>.</p> </span> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionprimerstrim> <div class=card> <div class=card-header id=headingprimerstrim> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#primerstrim aria-expanded aria-controls=primerstrim onclick="setAnchor('#primerstrim')"><span class=property-name>primerstrim</span></button> </h2> </div> <div id=primerstrim class="collapse property-definition-div" aria-labelledby=headingprimerstrim data-parent=#accordionprimerstrim> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#primerstrim onclick="anchorLink('primerstrim')">primerstrim</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionprimerstrim_mem> <div class=card> <div class=card-header id=headingprimerstrim_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#primerstrim_mem aria-expanded aria-controls=primerstrim_mem onclick="setAnchor('#primerstrim_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=primerstrim_mem class="collapse property-definition-div" aria-labelledby=headingprimerstrim_mem data-parent=#accordionprimerstrim_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#primerstrim onclick="anchorLink('primerstrim')">primerstrim</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#primerstrim_mem onclick="anchorLink('primerstrim_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1250</span><br> </div> </div> </div> </div> <div class=accordion id=accordionprimerstrim_time> <div class=card> <div class=card-header id=headingprimerstrim_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#primerstrim_time aria-expanded aria-controls=primerstrim_time onclick="setAnchor('#primerstrim_time')"><span class=property-name>time</span></button> </h2> </div> <div id=primerstrim_time class="collapse property-definition-div" aria-labelledby=headingprimerstrim_time data-parent=#accordionprimerstrim_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#primerstrim onclick="anchorLink('primerstrim')">primerstrim</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#primerstrim_time onclick="anchorLink('primerstrim_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionprimerstrim_conda> <div class=card> <div class=card-header id=headingprimerstrim_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#primerstrim_conda aria-expanded aria-controls=primerstrim_conda onclick="setAnchor('#primerstrim_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=primerstrim_conda class="collapse property-definition-div" aria-labelledby=headingprimerstrim_conda data-parent=#accordionprimerstrim_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#primerstrim onclick="anchorLink('primerstrim')">primerstrim</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#primerstrim_conda onclick="anchorLink('primerstrim_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/primerstrim.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_sequences> <div class=card> <div class=card-header id=headingconsensus_sequences> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_sequences aria-expanded aria-controls=consensus_sequences onclick="setAnchor('#consensus_sequences')"><span class=property-name>consensus_sequences</span></button> </h2> </div> <div id=consensus_sequences class="collapse property-definition-div" aria-labelledby=headingconsensus_sequences data-parent=#accordionconsensus_sequences> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences onclick="anchorLink('consensus_sequences')">consensus_sequences</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionconsensus_sequences_mem> <div class=card> <div class=card-header id=headingconsensus_sequences_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_sequences_mem aria-expanded aria-controls=consensus_sequences_mem onclick="setAnchor('#consensus_sequences_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=consensus_sequences_mem class="collapse property-definition-div" aria-labelledby=headingconsensus_sequences_mem data-parent=#accordionconsensus_sequences_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences onclick="anchorLink('consensus_sequences')">consensus_sequences</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences_mem onclick="anchorLink('consensus_sequences_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1250</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_sequences_time> <div class=card> <div class=card-header id=headingconsensus_sequences_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_sequences_time aria-expanded aria-controls=consensus_sequences_time onclick="setAnchor('#consensus_sequences_time')"><span class=property-name>time</span></button> </h2> </div> <div id=consensus_sequences_time class="collapse property-definition-div" aria-labelledby=headingconsensus_sequences_time data-parent=#accordionconsensus_sequences_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences onclick="anchorLink('consensus_sequences')">consensus_sequences</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences_time onclick="anchorLink('consensus_sequences_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_sequences_conda> <div class=card> <div class=card-header id=headingconsensus_sequences_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_sequences_conda aria-expanded aria-controls=consensus_sequences_conda onclick="setAnchor('#consensus_sequences_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=consensus_sequences_conda class="collapse property-definition-div" aria-labelledby=headingconsensus_sequences_conda data-parent=#accordionconsensus_sequences_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences onclick="anchorLink('consensus_sequences')">consensus_sequences</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences_conda onclick="anchorLink('consensus_sequences_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/smallgenomeutilities.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_sequences_min_coverage> <div class=card> <div class=card-header id=headingconsensus_sequences_min_coverage> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_sequences_min_coverage aria-expanded aria-controls=consensus_sequences_min_coverage onclick="setAnchor('#consensus_sequences_min_coverage')"><span class=property-name>min_coverage</span></button> </h2> </div> <div id=consensus_sequences_min_coverage class="collapse property-definition-div" aria-labelledby=headingconsensus_sequences_min_coverage data-parent=#accordionconsensus_sequences_min_coverage> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences onclick="anchorLink('consensus_sequences')">consensus_sequences</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences_min_coverage onclick="anchorLink('consensus_sequences_min_coverage')">min_coverage</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 50</span><br> <span class=description><p>Minimum read depth for reporting variants per locus.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_sequences_n_coverage> <div class=card> <div class=card-header id=headingconsensus_sequences_n_coverage> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_sequences_n_coverage aria-expanded aria-controls=consensus_sequences_n_coverage onclick="setAnchor('#consensus_sequences_n_coverage')"><span class=property-name>n_coverage</span></button> </h2> </div> <div id=consensus_sequences_n_coverage class="collapse property-definition-div" aria-labelledby=headingconsensus_sequences_n_coverage data-parent=#accordionconsensus_sequences_n_coverage> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences onclick="anchorLink('consensus_sequences')">consensus_sequences</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences_n_coverage onclick="anchorLink('consensus_sequences_n_coverage')">n_coverage</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 5</span><br> <span class=description><p>Read count below which ambiguous base ’n’ is reported.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_sequences_qual_thrd> <div class=card> <div class=card-header id=headingconsensus_sequences_qual_thrd> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_sequences_qual_thrd aria-expanded aria-controls=consensus_sequences_qual_thrd onclick="setAnchor('#consensus_sequences_qual_thrd')"><span class=property-name>qual_thrd</span></button> </h2> </div> <div id=consensus_sequences_qual_thrd class="collapse property-definition-div" aria-labelledby=headingconsensus_sequences_qual_thrd data-parent=#accordionconsensus_sequences_qual_thrd> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences onclick="anchorLink('consensus_sequences')">consensus_sequences</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences_qual_thrd onclick="anchorLink('consensus_sequences_qual_thrd')">qual_thrd</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 15</span><br> <span class=description><p>Minimum phred quality score for a base to be included.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_sequences_min_freq> <div class=card> <div class=card-header id=headingconsensus_sequences_min_freq> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_sequences_min_freq aria-expanded aria-controls=consensus_sequences_min_freq onclick="setAnchor('#consensus_sequences_min_freq')"><span class=property-name>min_freq</span></button> </h2> </div> <div id=consensus_sequences_min_freq class="collapse property-definition-div" aria-labelledby=headingconsensus_sequences_min_freq data-parent=#accordionconsensus_sequences_min_freq> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences onclick="anchorLink('consensus_sequences')">consensus_sequences</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_sequences_min_freq onclick="anchorLink('consensus_sequences_min_freq')">min_freq</a></div><span class="badge badge-dark value-type">Type: number</span> <span class="badge badge-success default-value">Default: 0.05</span><br> <span class=description><p>Minimum frequency for an ambiguous nucleotide.</p> </span> <p><span class="badge badge-light restriction numeric-restriction" id=consensus_sequences_min_freq_number>Value must be greater or equal to <code>0</code> and lesser or equal to <code>1</code></span></p> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_bcftools> <div class=card> <div class=card-header id=headingconsensus_bcftools> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_bcftools aria-expanded aria-controls=consensus_bcftools onclick="setAnchor('#consensus_bcftools')"><span class=property-name>consensus_bcftools</span></button> </h2> </div> <div id=consensus_bcftools class="collapse property-definition-div" aria-labelledby=headingconsensus_bcftools data-parent=#accordionconsensus_bcftools> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools onclick="anchorLink('consensus_bcftools')">consensus_bcftools</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionconsensus_bcftools_mem> <div class=card> <div class=card-header id=headingconsensus_bcftools_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_bcftools_mem aria-expanded aria-controls=consensus_bcftools_mem onclick="setAnchor('#consensus_bcftools_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=consensus_bcftools_mem class="collapse property-definition-div" aria-labelledby=headingconsensus_bcftools_mem data-parent=#accordionconsensus_bcftools_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools onclick="anchorLink('consensus_bcftools')">consensus_bcftools</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools_mem onclick="anchorLink('consensus_bcftools_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1250</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_bcftools_time> <div class=card> <div class=card-header id=headingconsensus_bcftools_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_bcftools_time aria-expanded aria-controls=consensus_bcftools_time onclick="setAnchor('#consensus_bcftools_time')"><span class=property-name>time</span></button> </h2> </div> <div id=consensus_bcftools_time class="collapse property-definition-div" aria-labelledby=headingconsensus_bcftools_time data-parent=#accordionconsensus_bcftools_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools onclick="anchorLink('consensus_bcftools')">consensus_bcftools</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools_time onclick="anchorLink('consensus_bcftools_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_bcftools_threads> <div class=card> <div class=card-header id=headingconsensus_bcftools_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_bcftools_threads aria-expanded aria-controls=consensus_bcftools_threads onclick="setAnchor('#consensus_bcftools_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=consensus_bcftools_threads class="collapse property-definition-div" aria-labelledby=headingconsensus_bcftools_threads data-parent=#accordionconsensus_bcftools_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools onclick="anchorLink('consensus_bcftools')">consensus_bcftools</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools_threads onclick="anchorLink('consensus_bcftools_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_bcftools_conda> <div class=card> <div class=card-header id=headingconsensus_bcftools_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_bcftools_conda aria-expanded aria-controls=consensus_bcftools_conda onclick="setAnchor('#consensus_bcftools_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=consensus_bcftools_conda class="collapse property-definition-div" aria-labelledby=headingconsensus_bcftools_conda data-parent=#accordionconsensus_bcftools_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools onclick="anchorLink('consensus_bcftools')">consensus_bcftools</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools_conda onclick="anchorLink('consensus_bcftools_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/bcftools.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_bcftools_max_coverage> <div class=card> <div class=card-header id=headingconsensus_bcftools_max_coverage> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_bcftools_max_coverage aria-expanded aria-controls=consensus_bcftools_max_coverage onclick="setAnchor('#consensus_bcftools_max_coverage')"><span class=property-name>max_coverage</span></button> </h2> </div> <div id=consensus_bcftools_max_coverage class="collapse property-definition-div" aria-labelledby=headingconsensus_bcftools_max_coverage data-parent=#accordionconsensus_bcftools_max_coverage> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools onclick="anchorLink('consensus_bcftools')">consensus_bcftools</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools_max_coverage onclick="anchorLink('consensus_bcftools_max_coverage')">max_coverage</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 10000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_bcftools_mask_coverage_threshold> <div class=card> <div class=card-header id=headingconsensus_bcftools_mask_coverage_threshold> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_bcftools_mask_coverage_threshold aria-expanded aria-controls=consensus_bcftools_mask_coverage_threshold onclick="setAnchor('#consensus_bcftools_mask_coverage_threshold')"><span class=property-name>mask_coverage_threshold</span></button> </h2> </div> <div id=consensus_bcftools_mask_coverage_threshold class="collapse property-definition-div" aria-labelledby=headingconsensus_bcftools_mask_coverage_threshold data-parent=#accordionconsensus_bcftools_mask_coverage_threshold> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools onclick="anchorLink('consensus_bcftools')">consensus_bcftools</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools_mask_coverage_threshold onclick="anchorLink('consensus_bcftools_mask_coverage_threshold')">mask_coverage_threshold</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 10</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconsensus_bcftools_ambiguous_base_coverage_threshold> <div class=card> <div class=card-header id=headingconsensus_bcftools_ambiguous_base_coverage_threshold> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consensus_bcftools_ambiguous_base_coverage_threshold aria-expanded aria-controls=consensus_bcftools_ambiguous_base_coverage_threshold onclick="setAnchor('#consensus_bcftools_ambiguous_base_coverage_threshold')"><span class=property-name>ambiguous_base_coverage_threshold</span></button> </h2> </div> <div id=consensus_bcftools_ambiguous_base_coverage_threshold class="collapse property-definition-div" aria-labelledby=headingconsensus_bcftools_ambiguous_base_coverage_threshold data-parent=#accordionconsensus_bcftools_ambiguous_base_coverage_threshold> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools onclick="anchorLink('consensus_bcftools')">consensus_bcftools</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consensus_bcftools_ambiguous_base_coverage_threshold onclick="anchorLink('consensus_bcftools_ambiguous_base_coverage_threshold')">ambiguous_base_coverage_threshold</a></div><span class="badge badge-dark value-type">Type: number</span> <span class="badge badge-success default-value">Default: 0.05</span><br> <p><span class="badge badge-light restriction numeric-restriction" id=consensus_bcftools_ambiguous_base_coverage_threshold_number>Value must be greater or equal to <code>0</code> and lesser or equal to <code>1</code></span></p> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionconsseq_QA> <div class=card> <div class=card-header id=headingconsseq_QA> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consseq_QA aria-expanded aria-controls=consseq_QA onclick="setAnchor('#consseq_QA')"><span class=property-name>consseq_QA</span></button> </h2> </div> <div id=consseq_QA class="collapse property-definition-div" aria-labelledby=headingconsseq_QA data-parent=#accordionconsseq_QA> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consseq_QA onclick="anchorLink('consseq_QA')">consseq_QA</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionconsseq_QA_mem> <div class=card> <div class=card-header id=headingconsseq_QA_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consseq_QA_mem aria-expanded aria-controls=consseq_QA_mem onclick="setAnchor('#consseq_QA_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=consseq_QA_mem class="collapse property-definition-div" aria-labelledby=headingconsseq_QA_mem data-parent=#accordionconsseq_QA_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consseq_QA onclick="anchorLink('consseq_QA')">consseq_QA</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consseq_QA_mem onclick="anchorLink('consseq_QA_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 4096</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconsseq_QA_time> <div class=card> <div class=card-header id=headingconsseq_QA_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consseq_QA_time aria-expanded aria-controls=consseq_QA_time onclick="setAnchor('#consseq_QA_time')"><span class=property-name>time</span></button> </h2> </div> <div id=consseq_QA_time class="collapse property-definition-div" aria-labelledby=headingconsseq_QA_time data-parent=#accordionconsseq_QA_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consseq_QA onclick="anchorLink('consseq_QA')">consseq_QA</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consseq_QA_time onclick="anchorLink('consseq_QA_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 30</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconsseq_QA_threads> <div class=card> <div class=card-header id=headingconsseq_QA_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consseq_QA_threads aria-expanded aria-controls=consseq_QA_threads onclick="setAnchor('#consseq_QA_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=consseq_QA_threads class="collapse property-definition-div" aria-labelledby=headingconsseq_QA_threads data-parent=#accordionconsseq_QA_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consseq_QA onclick="anchorLink('consseq_QA')">consseq_QA</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consseq_QA_threads onclick="anchorLink('consseq_QA_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionconsseq_QA_conda> <div class=card> <div class=card-header id=headingconsseq_QA_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#consseq_QA_conda aria-expanded aria-controls=consseq_QA_conda onclick="setAnchor('#consseq_QA_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=consseq_QA_conda class="collapse property-definition-div" aria-labelledby=headingconsseq_QA_conda data-parent=#accordionconsseq_QA_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consseq_QA onclick="anchorLink('consseq_QA')">consseq_QA</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#consseq_QA_conda onclick="anchorLink('consseq_QA_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/consseq_qa.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionframeshift_deletions_checks> <div class=card> <div class=card-header id=headingframeshift_deletions_checks> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#frameshift_deletions_checks aria-expanded aria-controls=frameshift_deletions_checks onclick="setAnchor('#frameshift_deletions_checks')"><span class=property-name>frameshift_deletions_checks</span></button> </h2> </div> <div id=frameshift_deletions_checks class="collapse property-definition-div" aria-labelledby=headingframeshift_deletions_checks data-parent=#accordionframeshift_deletions_checks> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#frameshift_deletions_checks onclick="anchorLink('frameshift_deletions_checks')">frameshift_deletions_checks</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionframeshift_deletions_checks_mem> <div class=card> <div class=card-header id=headingframeshift_deletions_checks_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#frameshift_deletions_checks_mem aria-expanded aria-controls=frameshift_deletions_checks_mem onclick="setAnchor('#frameshift_deletions_checks_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=frameshift_deletions_checks_mem class="collapse property-definition-div" aria-labelledby=headingframeshift_deletions_checks_mem data-parent=#accordionframeshift_deletions_checks_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#frameshift_deletions_checks onclick="anchorLink('frameshift_deletions_checks')">frameshift_deletions_checks</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#frameshift_deletions_checks_mem onclick="anchorLink('frameshift_deletions_checks_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1250</span><br> </div> </div> </div> </div> <div class=accordion id=accordionframeshift_deletions_checks_time> <div class=card> <div class=card-header id=headingframeshift_deletions_checks_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#frameshift_deletions_checks_time aria-expanded aria-controls=frameshift_deletions_checks_time onclick="setAnchor('#frameshift_deletions_checks_time')"><span class=property-name>time</span></button> </h2> </div> <div id=frameshift_deletions_checks_time class="collapse property-definition-div" aria-labelledby=headingframeshift_deletions_checks_time data-parent=#accordionframeshift_deletions_checks_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#frameshift_deletions_checks onclick="anchorLink('frameshift_deletions_checks')">frameshift_deletions_checks</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#frameshift_deletions_checks_time onclick="anchorLink('frameshift_deletions_checks_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 30</span><br> </div> </div> </div> </div> <div class=accordion id=accordionframeshift_deletions_checks_threads> <div class=card> <div class=card-header id=headingframeshift_deletions_checks_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#frameshift_deletions_checks_threads aria-expanded aria-controls=frameshift_deletions_checks_threads onclick="setAnchor('#frameshift_deletions_checks_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=frameshift_deletions_checks_threads class="collapse property-definition-div" aria-labelledby=headingframeshift_deletions_checks_threads data-parent=#accordionframeshift_deletions_checks_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#frameshift_deletions_checks onclick="anchorLink('frameshift_deletions_checks')">frameshift_deletions_checks</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#frameshift_deletions_checks_threads onclick="anchorLink('frameshift_deletions_checks_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionframeshift_deletions_checks_conda> <div class=card> <div class=card-header id=headingframeshift_deletions_checks_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#frameshift_deletions_checks_conda aria-expanded aria-controls=frameshift_deletions_checks_conda onclick="setAnchor('#frameshift_deletions_checks_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=frameshift_deletions_checks_conda class="collapse property-definition-div" aria-labelledby=headingframeshift_deletions_checks_conda data-parent=#accordionframeshift_deletions_checks_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#frameshift_deletions_checks onclick="anchorLink('frameshift_deletions_checks')">frameshift_deletions_checks</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#frameshift_deletions_checks_conda onclick="anchorLink('frameshift_deletions_checks_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/smallgenomeutilities.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionpaired_end_read_merger> <div class=card> <div class=card-header id=headingpaired_end_read_merger> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#paired_end_read_merger aria-expanded aria-controls=paired_end_read_merger onclick="setAnchor('#paired_end_read_merger')"><span class=property-name>paired_end_read_merger</span></button> </h2> </div> <div id=paired_end_read_merger class="collapse property-definition-div" aria-labelledby=headingpaired_end_read_merger data-parent=#accordionpaired_end_read_merger> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#paired_end_read_merger onclick="anchorLink('paired_end_read_merger')">paired_end_read_merger</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionpaired_end_read_merger_mem> <div class=card> <div class=card-header id=headingpaired_end_read_merger_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#paired_end_read_merger_mem aria-expanded aria-controls=paired_end_read_merger_mem onclick="setAnchor('#paired_end_read_merger_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=paired_end_read_merger_mem class="collapse property-definition-div" aria-labelledby=headingpaired_end_read_merger_mem data-parent=#accordionpaired_end_read_merger_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#paired_end_read_merger onclick="anchorLink('paired_end_read_merger')">paired_end_read_merger</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#paired_end_read_merger_mem onclick="anchorLink('paired_end_read_merger_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1250</span><br> </div> </div> </div> </div> <div class=accordion id=accordionpaired_end_read_merger_time> <div class=card> <div class=card-header id=headingpaired_end_read_merger_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#paired_end_read_merger_time aria-expanded aria-controls=paired_end_read_merger_time onclick="setAnchor('#paired_end_read_merger_time')"><span class=property-name>time</span></button> </h2> </div> <div id=paired_end_read_merger_time class="collapse property-definition-div" aria-labelledby=headingpaired_end_read_merger_time data-parent=#accordionpaired_end_read_merger_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#paired_end_read_merger onclick="anchorLink('paired_end_read_merger')">paired_end_read_merger</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#paired_end_read_merger_time onclick="anchorLink('paired_end_read_merger_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 30</span><br> </div> </div> </div> </div> <div class=accordion id=accordionpaired_end_read_merger_threads> <div class=card> <div class=card-header id=headingpaired_end_read_merger_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#paired_end_read_merger_threads aria-expanded aria-controls=paired_end_read_merger_threads onclick="setAnchor('#paired_end_read_merger_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=paired_end_read_merger_threads class="collapse property-definition-div" aria-labelledby=headingpaired_end_read_merger_threads data-parent=#accordionpaired_end_read_merger_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#paired_end_read_merger onclick="anchorLink('paired_end_read_merger')">paired_end_read_merger</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#paired_end_read_merger_threads onclick="anchorLink('paired_end_read_merger_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionpaired_end_read_merger_conda> <div class=card> <div class=card-header id=headingpaired_end_read_merger_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#paired_end_read_merger_conda aria-expanded aria-controls=paired_end_read_merger_conda onclick="setAnchor('#paired_end_read_merger_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=paired_end_read_merger_conda class="collapse property-definition-div" aria-labelledby=headingpaired_end_read_merger_conda data-parent=#accordionpaired_end_read_merger_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#paired_end_read_merger onclick="anchorLink('paired_end_read_merger')">paired_end_read_merger</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#paired_end_read_merger_conda onclick="anchorLink('paired_end_read_merger_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/paired_end_read_merger.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionbasecounts> <div class=card> <div class=card-header id=headingbasecounts> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#basecounts aria-expanded aria-controls=basecounts onclick="setAnchor('#basecounts')"><span class=property-name>basecounts</span></button> </h2> </div> <div id=basecounts class="collapse property-definition-div" aria-labelledby=headingbasecounts data-parent=#accordionbasecounts> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#basecounts onclick="anchorLink('basecounts')">basecounts</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionbasecounts_mem> <div class=card> <div class=card-header id=headingbasecounts_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#basecounts_mem aria-expanded aria-controls=basecounts_mem onclick="setAnchor('#basecounts_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=basecounts_mem class="collapse property-definition-div" aria-labelledby=headingbasecounts_mem data-parent=#accordionbasecounts_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#basecounts onclick="anchorLink('basecounts')">basecounts</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#basecounts_mem onclick="anchorLink('basecounts_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1250</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbasecounts_time> <div class=card> <div class=card-header id=headingbasecounts_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#basecounts_time aria-expanded aria-controls=basecounts_time onclick="setAnchor('#basecounts_time')"><span class=property-name>time</span></button> </h2> </div> <div id=basecounts_time class="collapse property-definition-div" aria-labelledby=headingbasecounts_time data-parent=#accordionbasecounts_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#basecounts onclick="anchorLink('basecounts')">basecounts</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#basecounts_time onclick="anchorLink('basecounts_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 30</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbasecounts_threads> <div class=card> <div class=card-header id=headingbasecounts_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#basecounts_threads aria-expanded aria-controls=basecounts_threads onclick="setAnchor('#basecounts_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=basecounts_threads class="collapse property-definition-div" aria-labelledby=headingbasecounts_threads data-parent=#accordionbasecounts_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#basecounts onclick="anchorLink('basecounts')">basecounts</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#basecounts_threads onclick="anchorLink('basecounts_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionbasecounts_conda> <div class=card> <div class=card-header id=headingbasecounts_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#basecounts_conda aria-expanded aria-controls=basecounts_conda onclick="setAnchor('#basecounts_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=basecounts_conda class="collapse property-definition-div" aria-labelledby=headingbasecounts_conda data-parent=#accordionbasecounts_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#basecounts onclick="anchorLink('basecounts')">basecounts</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#basecounts_conda onclick="anchorLink('basecounts_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/smallgenomeutilities.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordioncoverage> <div class=card> <div class=card-header id=headingcoverage> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage aria-expanded aria-controls=coverage onclick="setAnchor('#coverage')"><span class=property-name>coverage</span></button> </h2> </div> <div id=coverage class="collapse property-definition-div" aria-labelledby=headingcoverage data-parent=#accordioncoverage> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage onclick="anchorLink('coverage')">coverage</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordioncoverage_mem> <div class=card> <div class=card-header id=headingcoverage_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_mem aria-expanded aria-controls=coverage_mem onclick="setAnchor('#coverage_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=coverage_mem class="collapse property-definition-div" aria-labelledby=headingcoverage_mem data-parent=#accordioncoverage_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage onclick="anchorLink('coverage')">coverage</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_mem onclick="anchorLink('coverage_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1250</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_time> <div class=card> <div class=card-header id=headingcoverage_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_time aria-expanded aria-controls=coverage_time onclick="setAnchor('#coverage_time')"><span class=property-name>time</span></button> </h2> </div> <div id=coverage_time class="collapse property-definition-div" aria-labelledby=headingcoverage_time data-parent=#accordioncoverage_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage onclick="anchorLink('coverage')">coverage</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_time onclick="anchorLink('coverage_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 30</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_threads> <div class=card> <div class=card-header id=headingcoverage_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_threads aria-expanded aria-controls=coverage_threads onclick="setAnchor('#coverage_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=coverage_threads class="collapse property-definition-div" aria-labelledby=headingcoverage_threads data-parent=#accordioncoverage_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage onclick="anchorLink('coverage')">coverage</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_threads onclick="anchorLink('coverage_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_conda> <div class=card> <div class=card-header id=headingcoverage_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_conda aria-expanded aria-controls=coverage_conda onclick="setAnchor('#coverage_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=coverage_conda class="collapse property-definition-div" aria-labelledby=headingcoverage_conda data-parent=#accordioncoverage_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage onclick="anchorLink('coverage')">coverage</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_conda onclick="anchorLink('coverage_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/smallgenomeutilities.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionminor_variants> <div class=card> <div class=card-header id=headingminor_variants> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minor_variants aria-expanded aria-controls=minor_variants onclick="setAnchor('#minor_variants')"><span class=property-name>minor_variants</span></button> </h2> </div> <div id=minor_variants class="collapse property-definition-div" aria-labelledby=headingminor_variants data-parent=#accordionminor_variants> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minor_variants onclick="anchorLink('minor_variants')">minor_variants</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionminor_variants_mem> <div class=card> <div class=card-header id=headingminor_variants_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minor_variants_mem aria-expanded aria-controls=minor_variants_mem onclick="setAnchor('#minor_variants_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=minor_variants_mem class="collapse property-definition-div" aria-labelledby=headingminor_variants_mem data-parent=#accordionminor_variants_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minor_variants onclick="anchorLink('minor_variants')">minor_variants</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minor_variants_mem onclick="anchorLink('minor_variants_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionminor_variants_time> <div class=card> <div class=card-header id=headingminor_variants_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minor_variants_time aria-expanded aria-controls=minor_variants_time onclick="setAnchor('#minor_variants_time')"><span class=property-name>time</span></button> </h2> </div> <div id=minor_variants_time class="collapse property-definition-div" aria-labelledby=headingminor_variants_time data-parent=#accordionminor_variants_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minor_variants onclick="anchorLink('minor_variants')">minor_variants</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minor_variants_time onclick="anchorLink('minor_variants_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionminor_variants_threads> <div class=card> <div class=card-header id=headingminor_variants_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minor_variants_threads aria-expanded aria-controls=minor_variants_threads onclick="setAnchor('#minor_variants_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=minor_variants_threads class="collapse property-definition-div" aria-labelledby=headingminor_variants_threads data-parent=#accordionminor_variants_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minor_variants onclick="anchorLink('minor_variants')">minor_variants</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minor_variants_threads onclick="anchorLink('minor_variants_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionminor_variants_conda> <div class=card> <div class=card-header id=headingminor_variants_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minor_variants_conda aria-expanded aria-controls=minor_variants_conda onclick="setAnchor('#minor_variants_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=minor_variants_conda class="collapse property-definition-div" aria-labelledby=headingminor_variants_conda data-parent=#accordionminor_variants_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minor_variants onclick="anchorLink('minor_variants')">minor_variants</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minor_variants_conda onclick="anchorLink('minor_variants_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/smallgenomeutilities.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionminor_variants_min_coverage> <div class=card> <div class=card-header id=headingminor_variants_min_coverage> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minor_variants_min_coverage aria-expanded aria-controls=minor_variants_min_coverage onclick="setAnchor('#minor_variants_min_coverage')"><span class=property-name>min_coverage</span></button> </h2> </div> <div id=minor_variants_min_coverage class="collapse property-definition-div" aria-labelledby=headingminor_variants_min_coverage data-parent=#accordionminor_variants_min_coverage> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minor_variants onclick="anchorLink('minor_variants')">minor_variants</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minor_variants_min_coverage onclick="anchorLink('minor_variants_min_coverage')">min_coverage</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 100</span><br> <span class=description><p>Minimum read depth for reporting variants per locus.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=minor_variants_min_coverage_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">50</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionminor_variants_frequencies> <div class=card> <div class=card-header id=headingminor_variants_frequencies> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#minor_variants_frequencies aria-expanded aria-controls=minor_variants_frequencies onclick="setAnchor('#minor_variants_frequencies')"><span class=property-name>frequencies</span></button> </h2> </div> <div id=minor_variants_frequencies class="collapse property-definition-div" aria-labelledby=headingminor_variants_frequencies data-parent=#accordionminor_variants_frequencies> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minor_variants onclick="anchorLink('minor_variants')">minor_variants</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#minor_variants_frequencies onclick="anchorLink('minor_variants_frequencies')">frequencies</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>Output a numpy array file containing frequencies of all bases, including gaps and also the most abundant base across samples.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=minor_variants_frequencies_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_intervals> <div class=card> <div class=card-header id=headingcoverage_intervals> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_intervals aria-expanded aria-controls=coverage_intervals onclick="setAnchor('#coverage_intervals')"><span class=property-name>coverage_intervals</span></button> </h2> </div> <div id=coverage_intervals class="collapse property-definition-div" aria-labelledby=headingcoverage_intervals data-parent=#accordioncoverage_intervals> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals onclick="anchorLink('coverage_intervals')">coverage_intervals</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordioncoverage_intervals_mem> <div class=card> <div class=card-header id=headingcoverage_intervals_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_intervals_mem aria-expanded aria-controls=coverage_intervals_mem onclick="setAnchor('#coverage_intervals_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=coverage_intervals_mem class="collapse property-definition-div" aria-labelledby=headingcoverage_intervals_mem data-parent=#accordioncoverage_intervals_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals onclick="anchorLink('coverage_intervals')">coverage_intervals</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals_mem onclick="anchorLink('coverage_intervals_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1000</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_intervals_time> <div class=card> <div class=card-header id=headingcoverage_intervals_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_intervals_time aria-expanded aria-controls=coverage_intervals_time onclick="setAnchor('#coverage_intervals_time')"><span class=property-name>time</span></button> </h2> </div> <div id=coverage_intervals_time class="collapse property-definition-div" aria-labelledby=headingcoverage_intervals_time data-parent=#accordioncoverage_intervals_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals onclick="anchorLink('coverage_intervals')">coverage_intervals</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals_time onclick="anchorLink('coverage_intervals_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 30</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_intervals_threads> <div class=card> <div class=card-header id=headingcoverage_intervals_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_intervals_threads aria-expanded aria-controls=coverage_intervals_threads onclick="setAnchor('#coverage_intervals_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=coverage_intervals_threads class="collapse property-definition-div" aria-labelledby=headingcoverage_intervals_threads data-parent=#accordioncoverage_intervals_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals onclick="anchorLink('coverage_intervals')">coverage_intervals</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals_threads onclick="anchorLink('coverage_intervals_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_intervals_conda> <div class=card> <div class=card-header id=headingcoverage_intervals_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_intervals_conda aria-expanded aria-controls=coverage_intervals_conda onclick="setAnchor('#coverage_intervals_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=coverage_intervals_conda class="collapse property-definition-div" aria-labelledby=headingcoverage_intervals_conda data-parent=#accordioncoverage_intervals_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals onclick="anchorLink('coverage_intervals')">coverage_intervals</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals_conda onclick="anchorLink('coverage_intervals_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/smallgenomeutilities.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_intervals_overlap> <div class=card> <div class=card-header id=headingcoverage_intervals_overlap> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_intervals_overlap aria-expanded aria-controls=coverage_intervals_overlap onclick="setAnchor('#coverage_intervals_overlap')"><span class=property-name>overlap</span></button> </h2> </div> <div id=coverage_intervals_overlap class="collapse property-definition-div" aria-labelledby=headingcoverage_intervals_overlap data-parent=#accordioncoverage_intervals_overlap> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals onclick="anchorLink('coverage_intervals')">coverage_intervals</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals_overlap onclick="anchorLink('coverage_intervals_overlap')">overlap</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>Construct intervals based on overlapping windows of the read alignment. By default, regions with high coverage are built based on the position-wise read depth.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=coverage_intervals_overlap_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_intervals_coverage> <div class=card> <div class=card-header id=headingcoverage_intervals_coverage> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_intervals_coverage aria-expanded aria-controls=coverage_intervals_coverage onclick="setAnchor('#coverage_intervals_coverage')"><span class=property-name>coverage</span></button> </h2> </div> <div id=coverage_intervals_coverage class="collapse property-definition-div" aria-labelledby=headingcoverage_intervals_coverage data-parent=#accordioncoverage_intervals_coverage> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals onclick="anchorLink('coverage_intervals')">coverage_intervals</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals_coverage onclick="anchorLink('coverage_intervals_coverage')">coverage</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 50</span><br> <span class=description><p>Minimum read depth. A region spanning the reference genome is returned if <code>coverage</code> is set to 0.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=coverage_intervals_coverage_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">0</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordioncoverage_intervals_liberal> <div class=card> <div class=card-header id=headingcoverage_intervals_liberal> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#coverage_intervals_liberal aria-expanded aria-controls=coverage_intervals_liberal onclick="setAnchor('#coverage_intervals_liberal')"><span class=property-name>liberal</span></button> </h2> </div> <div id=coverage_intervals_liberal class="collapse property-definition-div" aria-labelledby=headingcoverage_intervals_liberal data-parent=#accordioncoverage_intervals_liberal> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals onclick="anchorLink('coverage_intervals')">coverage_intervals</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#coverage_intervals_liberal onclick="anchorLink('coverage_intervals_liberal')">liberal</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: true</span><br> <span class=description><p>Indicate whether to apply a more liberal shifting on intervals’ right-endpoint.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=coverage_intervals_liberal_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">False</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionsnv> <div class=card> <div class=card-header id=headingsnv> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#snv aria-expanded aria-controls=snv onclick="setAnchor('#snv')"><span class=property-name>snv</span></button> </h2> </div> <div id=snv class="collapse property-definition-div" aria-labelledby=headingsnv data-parent=#accordionsnv> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv onclick="anchorLink('snv')">snv</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionsnv_mem> <div class=card> <div class=card-header id=headingsnv_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#snv_mem aria-expanded aria-controls=snv_mem onclick="setAnchor('#snv_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=snv_mem class="collapse property-definition-div" aria-labelledby=headingsnv_mem data-parent=#accordionsnv_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv onclick="anchorLink('snv')">snv</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv_mem onclick="anchorLink('snv_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 10000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionsnv_time> <div class=card> <div class=card-header id=headingsnv_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#snv_time aria-expanded aria-controls=snv_time onclick="setAnchor('#snv_time')"><span class=property-name>time</span></button> </h2> </div> <div id=snv_time class="collapse property-definition-div" aria-labelledby=headingsnv_time data-parent=#accordionsnv_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv onclick="anchorLink('snv')">snv</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv_time onclick="anchorLink('snv_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 2880</span><br> </div> </div> </div> </div> <div class=accordion id=accordionsnv_threads> <div class=card> <div class=card-header id=headingsnv_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#snv_threads aria-expanded aria-controls=snv_threads onclick="setAnchor('#snv_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=snv_threads class="collapse property-definition-div" aria-labelledby=headingsnv_threads data-parent=#accordionsnv_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv onclick="anchorLink('snv')">snv</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv_threads onclick="anchorLink('snv_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionsnv_conda> <div class=card> <div class=card-header id=headingsnv_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#snv_conda aria-expanded aria-controls=snv_conda onclick="setAnchor('#snv_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=snv_conda class="collapse property-definition-div" aria-labelledby=headingsnv_conda data-parent=#accordionsnv_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv onclick="anchorLink('snv')">snv</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv_conda onclick="anchorLink('snv_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/snv.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionsnv_consensus> <div class=card> <div class=card-header id=headingsnv_consensus> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#snv_consensus aria-expanded aria-controls=snv_consensus onclick="setAnchor('#snv_consensus')"><span class=property-name>consensus</span></button> </h2> </div> <div id=snv_consensus class="collapse property-definition-div" aria-labelledby=headingsnv_consensus data-parent=#accordionsnv_consensus> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv onclick="anchorLink('snv')">snv</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv_consensus onclick="anchorLink('snv_consensus')">consensus</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: true</span><br> <span class=description><p>Indicate whether to use the cohort-consensus sequence from the analyzed samples (output from <code>minor_variants</code> rule located in the cohort-wide output <code>results/cohort_onsensus.fasta</code>) or the reference sequence by setting this option to False.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=snv_consensus_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">False</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionsnv_alpha> <div class=card> <div class=card-header id=headingsnv_alpha> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#snv_alpha aria-expanded aria-controls=snv_alpha onclick="setAnchor('#snv_alpha')"><span class=property-name>alpha</span></button> </h2> </div> <div id=snv_alpha class="collapse property-definition-div" aria-labelledby=headingsnv_alpha data-parent=#accordionsnv_alpha> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv onclick="anchorLink('snv')">snv</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv_alpha onclick="anchorLink('snv_alpha')">alpha</a></div><span class="badge badge-dark value-type">Type: number</span> <span class="badge badge-success default-value">Default: 0.1</span><br> <span class=description><p>Hyperparameter used for instantiating a new cluster.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionsnv_ignore_indels> <div class=card> <div class=card-header id=headingsnv_ignore_indels> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#snv_ignore_indels aria-expanded aria-controls=snv_ignore_indels onclick="setAnchor('#snv_ignore_indels')"><span class=property-name>ignore_indels</span></button> </h2> </div> <div id=snv_ignore_indels class="collapse property-definition-div" aria-labelledby=headingsnv_ignore_indels data-parent=#accordionsnv_ignore_indels> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv onclick="anchorLink('snv')">snv</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv_ignore_indels onclick="anchorLink('snv_ignore_indels')">ignore_indels</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>Ignore SNVs adjacent to indels.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionsnv_posterior_threshold> <div class=card> <div class=card-header id=headingsnv_posterior_threshold> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#snv_posterior_threshold aria-expanded aria-controls=snv_posterior_threshold onclick="setAnchor('#snv_posterior_threshold')"><span class=property-name>posterior_threshold</span></button> </h2> </div> <div id=snv_posterior_threshold class="collapse property-definition-div" aria-labelledby=headingsnv_posterior_threshold data-parent=#accordionsnv_posterior_threshold> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv onclick="anchorLink('snv')">snv</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv_posterior_threshold onclick="anchorLink('snv_posterior_threshold')">posterior_threshold</a></div><span class="badge badge-dark value-type">Type: number</span> <span class="badge badge-success default-value">Default: 0.9</span><br> <p><span class="badge badge-light restriction numeric-restriction" id=snv_posterior_threshold_number>Value must be greater or equal to <code>0</code> and lesser or equal to <code>1</code></span></p> </div> </div> </div> </div> <div class=accordion id=accordionsnv_coverage> <div class=card> <div class=card-header id=headingsnv_coverage> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#snv_coverage aria-expanded aria-controls=snv_coverage onclick="setAnchor('#snv_coverage')"><span class=property-name>coverage</span></button> </h2> </div> <div id=snv_coverage class="collapse property-definition-div" aria-labelledby=headingsnv_coverage data-parent=#accordionsnv_coverage> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv onclick="anchorLink('snv')">snv</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv_coverage onclick="anchorLink('snv_coverage')">coverage</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 0</span><br> <span class=description><p>Omit windows with coverage less than this value.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=snv_coverage_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">50</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionsnv_shift> <div class=card> <div class=card-header id=headingsnv_shift> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#snv_shift aria-expanded aria-controls=snv_shift onclick="setAnchor('#snv_shift')"><span class=property-name>shift</span></button> </h2> </div> <div id=snv_shift class="collapse property-definition-div" aria-labelledby=headingsnv_shift data-parent=#accordionsnv_shift> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv onclick="anchorLink('snv')">snv</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv_shift onclick="anchorLink('snv_shift')">shift</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 3</span><br> <span class=description><p>ShoRAH performs local haplotype reconstruction on windows of the read alignment. The overlap between these windows is defined by the window shifts. By default, it is set to 3, i.e., apart from flanking regions each position is covered by 3 windows.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionsnv_keep_files> <div class=card> <div class=card-header id=headingsnv_keep_files> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#snv_keep_files aria-expanded aria-controls=snv_keep_files onclick="setAnchor('#snv_keep_files')"><span class=property-name>keep_files</span></button> </h2> </div> <div id=snv_keep_files class="collapse property-definition-div" aria-labelledby=headingsnv_keep_files data-parent=#accordionsnv_keep_files> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv onclick="anchorLink('snv')">snv</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv_keep_files onclick="anchorLink('snv_keep_files')">keep_files</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>Indicate whether to move files produced in previous/interrupted runs to subdirectory named <code>old</code></p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=snv_keep_files_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionsnv_localscratch> <div class=card> <div class=card-header id=headingsnv_localscratch> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#snv_localscratch aria-expanded aria-controls=snv_localscratch onclick="setAnchor('#snv_localscratch')"><span class=property-name>localscratch</span></button> </h2> </div> <div id=snv_localscratch class="collapse property-definition-div" aria-labelledby=headingsnv_localscratch data-parent=#accordionsnv_localscratch> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv onclick="anchorLink('snv')">snv</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#snv_localscratch onclick="anchorLink('snv_localscratch')">localscratch</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionsamtools_index> <div class=card> <div class=card-header id=headingsamtools_index> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#samtools_index aria-expanded aria-controls=samtools_index onclick="setAnchor('#samtools_index')"><span class=property-name>samtools_index</span></button> </h2> </div> <div id=samtools_index class="collapse property-definition-div" aria-labelledby=headingsamtools_index data-parent=#accordionsamtools_index> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#samtools_index onclick="anchorLink('samtools_index')">samtools_index</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionsamtools_index_mem> <div class=card> <div class=card-header id=headingsamtools_index_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#samtools_index_mem aria-expanded aria-controls=samtools_index_mem onclick="setAnchor('#samtools_index_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=samtools_index_mem class="collapse property-definition-div" aria-labelledby=headingsamtools_index_mem data-parent=#accordionsamtools_index_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#samtools_index onclick="anchorLink('samtools_index')">samtools_index</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#samtools_index_mem onclick="anchorLink('samtools_index_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 2000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionsamtools_index_time> <div class=card> <div class=card-header id=headingsamtools_index_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#samtools_index_time aria-expanded aria-controls=samtools_index_time onclick="setAnchor('#samtools_index_time')"><span class=property-name>time</span></button> </h2> </div> <div id=samtools_index_time class="collapse property-definition-div" aria-labelledby=headingsamtools_index_time data-parent=#accordionsamtools_index_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#samtools_index onclick="anchorLink('samtools_index')">samtools_index</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#samtools_index_time onclick="anchorLink('samtools_index_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 20</span><br> </div> </div> </div> </div> <div class=accordion id=accordionsamtools_index_conda> <div class=card> <div class=card-header id=headingsamtools_index_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#samtools_index_conda aria-expanded aria-controls=samtools_index_conda onclick="setAnchor('#samtools_index_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=samtools_index_conda class="collapse property-definition-div" aria-labelledby=headingsamtools_index_conda data-parent=#accordionsamtools_index_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#samtools_index onclick="anchorLink('samtools_index')">samtools_index</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#samtools_index_conda onclick="anchorLink('samtools_index_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/lofreq.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionviloca> <div class=card> <div class=card-header id=headingviloca> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#viloca aria-expanded aria-controls=viloca onclick="setAnchor('#viloca')"><span class=property-name>viloca</span></button> </h2> </div> <div id=viloca class="collapse property-definition-div" aria-labelledby=headingviloca data-parent=#accordionviloca> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca onclick="anchorLink('viloca')">viloca</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionviloca_mem> <div class=card> <div class=card-header id=headingviloca_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#viloca_mem aria-expanded aria-controls=viloca_mem onclick="setAnchor('#viloca_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=viloca_mem class="collapse property-definition-div" aria-labelledby=headingviloca_mem data-parent=#accordionviloca_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca onclick="anchorLink('viloca')">viloca</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca_mem onclick="anchorLink('viloca_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 10000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionviloca_threads> <div class=card> <div class=card-header id=headingviloca_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#viloca_threads aria-expanded aria-controls=viloca_threads onclick="setAnchor('#viloca_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=viloca_threads class="collapse property-definition-div" aria-labelledby=headingviloca_threads data-parent=#accordionviloca_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca onclick="anchorLink('viloca')">viloca</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca_threads onclick="anchorLink('viloca_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionviloca_time> <div class=card> <div class=card-header id=headingviloca_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#viloca_time aria-expanded aria-controls=viloca_time onclick="setAnchor('#viloca_time')"><span class=property-name>time</span></button> </h2> </div> <div id=viloca_time class="collapse property-definition-div" aria-labelledby=headingviloca_time data-parent=#accordionviloca_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca onclick="anchorLink('viloca')">viloca</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca_time onclick="anchorLink('viloca_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 2880</span><br> </div> </div> </div> </div> <div class=accordion id=accordionviloca_conda> <div class=card> <div class=card-header id=headingviloca_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#viloca_conda aria-expanded aria-controls=viloca_conda onclick="setAnchor('#viloca_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=viloca_conda class="collapse property-definition-div" aria-labelledby=headingviloca_conda data-parent=#accordionviloca_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca onclick="anchorLink('viloca')">viloca</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca_conda onclick="anchorLink('viloca_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/viloca.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionviloca_consensus> <div class=card> <div class=card-header id=headingviloca_consensus> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#viloca_consensus aria-expanded aria-controls=viloca_consensus onclick="setAnchor('#viloca_consensus')"><span class=property-name>consensus</span></button> </h2> </div> <div id=viloca_consensus class="collapse property-definition-div" aria-labelledby=headingviloca_consensus data-parent=#accordionviloca_consensus> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca onclick="anchorLink('viloca')">viloca</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca_consensus onclick="anchorLink('viloca_consensus')">consensus</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>Indicate whether to use the cohort-consensus sequence from the analyzed samples (output from <code>minor_variants</code> rule located in the cohort-wide output <code>results/cohort_onsensus.fasta</code>) or the reference sequence by setting this option to False.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=viloca_consensus_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">False</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionviloca_merge_paired_end_reads> <div class=card> <div class=card-header id=headingviloca_merge_paired_end_reads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#viloca_merge_paired_end_reads aria-expanded aria-controls=viloca_merge_paired_end_reads onclick="setAnchor('#viloca_merge_paired_end_reads')"><span class=property-name>merge_paired_end_reads</span></button> </h2> </div> <div id=viloca_merge_paired_end_reads class="collapse property-definition-div" aria-labelledby=headingviloca_merge_paired_end_reads data-parent=#accordionviloca_merge_paired_end_reads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca onclick="anchorLink('viloca')">viloca</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca_merge_paired_end_reads onclick="anchorLink('viloca_merge_paired_end_reads')">merge_paired_end_reads</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>Merge paired-end reads in the preprocessing. This is a preprocessing snakemake rule.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=viloca_merge_paired_end_reads_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">False</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionviloca_shift> <div class=card> <div class=card-header id=headingviloca_shift> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#viloca_shift aria-expanded aria-controls=viloca_shift onclick="setAnchor('#viloca_shift')"><span class=property-name>shift</span></button> </h2> </div> <div id=viloca_shift class="collapse property-definition-div" aria-labelledby=headingviloca_shift data-parent=#accordionviloca_shift> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca onclick="anchorLink('viloca')">viloca</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca_shift onclick="anchorLink('viloca_shift')">shift</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 3</span><br> <span class=description><p>VILOCA performs local haplotype reconstruction on windows of the read alignment. The overlap between these windows is defined by the window shifts. By default, it is set to 3, i.e., apart from flanking regions each position is covered by 3 windows.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionviloca_insert_bedfile> <div class=card> <div class=card-header id=headingviloca_insert_bedfile> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#viloca_insert_bedfile aria-expanded aria-controls=viloca_insert_bedfile onclick="setAnchor('#viloca_insert_bedfile')"><span class=property-name>insert_bedfile</span></button> </h2> </div> <div id=viloca_insert_bedfile class="collapse property-definition-div" aria-labelledby=headingviloca_insert_bedfile data-parent=#accordionviloca_insert_bedfile> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca onclick="anchorLink('viloca')">viloca</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca_insert_bedfile onclick="anchorLink('viloca_insert_bedfile')">insert_bedfile</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "None"</span><br> <span class=description><p>VILOCA performs local haplotype reconstruction on windows of the read alignment. In a first step the alignment is tiled into local regions. This can be done uniformly then set this value None, otherwise path to an (optional) insert file (primer tiling strategy)</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionviloca_mode> <div class=card> <div class=card-header id=headingviloca_mode> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#viloca_mode aria-expanded aria-controls=viloca_mode onclick="setAnchor('#viloca_mode')"><span class=property-name>mode</span></button> </h2> </div> <div id=viloca_mode class="collapse property-definition-div" aria-labelledby=headingviloca_mode data-parent=#accordionviloca_mode> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca onclick="anchorLink('viloca')">viloca</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca_mode onclick="anchorLink('viloca_mode')">mode</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "use_quality_scores"</span><br> <span class=description><p>Mode in which to run VILOCA: shorah, learn<em>error</em>params, use<em>quality</em>scores. If quality scores are available, we recommend this option</p> </span><div class=enum-value id=viloca_mode_enum> <h4>Must be one of:</h4> <ul class=list-group><li class="list-group-item enum-item">"shorah"</li><li class="list-group-item enum-item">"learn_error_params"</li><li class="list-group-item enum-item">"use_quality_scores"</li></ul> </div> </div> </div> </div> </div> <div class=accordion id=accordionviloca_extra> <div class=card> <div class=card-header id=headingviloca_extra> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#viloca_extra aria-expanded aria-controls=viloca_extra onclick="setAnchor('#viloca_extra')"><span class=property-name>extra</span></button> </h2> </div> <div id=viloca_extra class="collapse property-definition-div" aria-labelledby=headingviloca_extra data-parent=#accordionviloca_extra> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca onclick="anchorLink('viloca')">viloca</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#viloca_extra onclick="anchorLink('viloca_extra')">extra</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>Pass additional options to run <code>viloca</code></p> </span> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionlofreq> <div class=card> <div class=card-header id=headinglofreq> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#lofreq aria-expanded aria-controls=lofreq onclick="setAnchor('#lofreq')"><span class=property-name>lofreq</span></button> </h2> </div> <div id=lofreq class="collapse property-definition-div" aria-labelledby=headinglofreq data-parent=#accordionlofreq> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#lofreq onclick="anchorLink('lofreq')">lofreq</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionlofreq_mem> <div class=card> <div class=card-header id=headinglofreq_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#lofreq_mem aria-expanded aria-controls=lofreq_mem onclick="setAnchor('#lofreq_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=lofreq_mem class="collapse property-definition-div" aria-labelledby=headinglofreq_mem data-parent=#accordionlofreq_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#lofreq onclick="anchorLink('lofreq')">lofreq</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#lofreq_mem onclick="anchorLink('lofreq_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 2000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionlofreq_time> <div class=card> <div class=card-header id=headinglofreq_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#lofreq_time aria-expanded aria-controls=lofreq_time onclick="setAnchor('#lofreq_time')"><span class=property-name>time</span></button> </h2> </div> <div id=lofreq_time class="collapse property-definition-div" aria-labelledby=headinglofreq_time data-parent=#accordionlofreq_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#lofreq onclick="anchorLink('lofreq')">lofreq</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#lofreq_time onclick="anchorLink('lofreq_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 60</span><br> </div> </div> </div> </div> <div class=accordion id=accordionlofreq_conda> <div class=card> <div class=card-header id=headinglofreq_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#lofreq_conda aria-expanded aria-controls=lofreq_conda onclick="setAnchor('#lofreq_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=lofreq_conda class="collapse property-definition-div" aria-labelledby=headinglofreq_conda data-parent=#accordionlofreq_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#lofreq onclick="anchorLink('lofreq')">lofreq</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#lofreq_conda onclick="anchorLink('lofreq_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/lofreq.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionlofreq_consensus> <div class=card> <div class=card-header id=headinglofreq_consensus> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#lofreq_consensus aria-expanded aria-controls=lofreq_consensus onclick="setAnchor('#lofreq_consensus')"><span class=property-name>consensus</span></button> </h2> </div> <div id=lofreq_consensus class="collapse property-definition-div" aria-labelledby=headinglofreq_consensus data-parent=#accordionlofreq_consensus> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#lofreq onclick="anchorLink('lofreq')">lofreq</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#lofreq_consensus onclick="anchorLink('lofreq_consensus')">consensus</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: true</span><br> <span class=description><p>Indicate whether to use the cohort-consensus sequence from the analyzed samples (output from <code>minor_variants</code> rule located in the cohort-wide output <code>results/cohort_onsensus.fasta</code>) or the reference sequence by setting this option to False.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=lofreq_consensus_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">False</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionlofreq_extra> <div class=card> <div class=card-header id=headinglofreq_extra> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#lofreq_extra aria-expanded aria-controls=lofreq_extra onclick="setAnchor('#lofreq_extra')"><span class=property-name>extra</span></button> </h2> </div> <div id=lofreq_extra class="collapse property-definition-div" aria-labelledby=headinglofreq_extra data-parent=#accordionlofreq_extra> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#lofreq onclick="anchorLink('lofreq')">lofreq</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#lofreq_extra onclick="anchorLink('lofreq_extra')">extra</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>Pass additional options to run <code>lofreq call</code></p> </span> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionalignment_coverage> <div class=card> <div class=card-header id=headingalignment_coverage> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#alignment_coverage aria-expanded aria-controls=alignment_coverage onclick="setAnchor('#alignment_coverage')"><span class=property-name>alignment_coverage</span></button> </h2> </div> <div id=alignment_coverage class="collapse property-definition-div" aria-labelledby=headingalignment_coverage data-parent=#accordionalignment_coverage> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#alignment_coverage onclick="anchorLink('alignment_coverage')">alignment_coverage</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionalignment_coverage_mem> <div class=card> <div class=card-header id=headingalignment_coverage_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#alignment_coverage_mem aria-expanded aria-controls=alignment_coverage_mem onclick="setAnchor('#alignment_coverage_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=alignment_coverage_mem class="collapse property-definition-div" aria-labelledby=headingalignment_coverage_mem data-parent=#accordionalignment_coverage_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#alignment_coverage onclick="anchorLink('alignment_coverage')">alignment_coverage</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#alignment_coverage_mem onclick="anchorLink('alignment_coverage_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionalignment_coverage_time> <div class=card> <div class=card-header id=headingalignment_coverage_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#alignment_coverage_time aria-expanded aria-controls=alignment_coverage_time onclick="setAnchor('#alignment_coverage_time')"><span class=property-name>time</span></button> </h2> </div> <div id=alignment_coverage_time class="collapse property-definition-div" aria-labelledby=headingalignment_coverage_time data-parent=#accordionalignment_coverage_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#alignment_coverage onclick="anchorLink('alignment_coverage')">alignment_coverage</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#alignment_coverage_time onclick="anchorLink('alignment_coverage_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 60</span><br> </div> </div> </div> </div> <div class=accordion id=accordionalignment_coverage_conda> <div class=card> <div class=card-header id=headingalignment_coverage_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#alignment_coverage_conda aria-expanded aria-controls=alignment_coverage_conda onclick="setAnchor('#alignment_coverage_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=alignment_coverage_conda class="collapse property-definition-div" aria-labelledby=headingalignment_coverage_conda data-parent=#accordionalignment_coverage_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#alignment_coverage onclick="anchorLink('alignment_coverage')">alignment_coverage</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#alignment_coverage_conda onclick="anchorLink('alignment_coverage_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/smallgenomeutilities.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionalignment_coverage_coverage> <div class=card> <div class=card-header id=headingalignment_coverage_coverage> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#alignment_coverage_coverage aria-expanded aria-controls=alignment_coverage_coverage onclick="setAnchor('#alignment_coverage_coverage')"><span class=property-name>coverage</span></button> </h2> </div> <div id=alignment_coverage_coverage class="collapse property-definition-div" aria-labelledby=headingalignment_coverage_coverage data-parent=#accordionalignment_coverage_coverage> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#alignment_coverage onclick="anchorLink('alignment_coverage')">alignment_coverage</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#alignment_coverage_coverage onclick="anchorLink('alignment_coverage_coverage')">coverage</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 5</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionstats> <div class=card> <div class=card-header id=headingstats> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#stats aria-expanded aria-controls=stats onclick="setAnchor('#stats')"><span class=property-name>stats</span></button> </h2> </div> <div id=stats class="collapse property-definition-div" aria-labelledby=headingstats data-parent=#accordionstats> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#stats onclick="anchorLink('stats')">stats</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionstats_conda> <div class=card> <div class=card-header id=headingstats_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#stats_conda aria-expanded aria-controls=stats_conda onclick="setAnchor('#stats_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=stats_conda class="collapse property-definition-div" aria-labelledby=headingstats_conda data-parent=#accordionstats_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#stats onclick="anchorLink('stats')">stats</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#stats_conda onclick="anchorLink('stats_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/sam2bam.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionsavage> <div class=card> <div class=card-header id=headingsavage> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#savage aria-expanded aria-controls=savage onclick="setAnchor('#savage')"><span class=property-name>savage</span></button> </h2> </div> <div id=savage class="collapse property-definition-div" aria-labelledby=headingsavage data-parent=#accordionsavage> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#savage onclick="anchorLink('savage')">savage</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <span class=description><p><strong>NOTE</strong> This rule only works in Linux.</p> </span> <div class=accordion id=accordionsavage_mem> <div class=card> <div class=card-header id=headingsavage_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#savage_mem aria-expanded aria-controls=savage_mem onclick="setAnchor('#savage_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=savage_mem class="collapse property-definition-div" aria-labelledby=headingsavage_mem data-parent=#accordionsavage_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#savage onclick="anchorLink('savage')">savage</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#savage_mem onclick="anchorLink('savage_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 10000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionsavage_time> <div class=card> <div class=card-header id=headingsavage_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#savage_time aria-expanded aria-controls=savage_time onclick="setAnchor('#savage_time')"><span class=property-name>time</span></button> </h2> </div> <div id=savage_time class="collapse property-definition-div" aria-labelledby=headingsavage_time data-parent=#accordionsavage_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#savage onclick="anchorLink('savage')">savage</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#savage_time onclick="anchorLink('savage_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1435</span><br> </div> </div> </div> </div> <div class=accordion id=accordionsavage_threads> <div class=card> <div class=card-header id=headingsavage_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#savage_threads aria-expanded aria-controls=savage_threads onclick="setAnchor('#savage_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=savage_threads class="collapse property-definition-div" aria-labelledby=headingsavage_threads data-parent=#accordionsavage_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#savage onclick="anchorLink('savage')">savage</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#savage_threads onclick="anchorLink('savage_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionsavage_conda> <div class=card> <div class=card-header id=headingsavage_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#savage_conda aria-expanded aria-controls=savage_conda onclick="setAnchor('#savage_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=savage_conda class="collapse property-definition-div" aria-labelledby=headingsavage_conda data-parent=#accordionsavage_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#savage onclick="anchorLink('savage')">savage</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#savage_conda onclick="anchorLink('savage_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/savage.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionsavage_split> <div class=card> <div class=card-header id=headingsavage_split> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#savage_split aria-expanded aria-controls=savage_split onclick="setAnchor('#savage_split')"><span class=property-name>split</span></button> </h2> </div> <div id=savage_split class="collapse property-definition-div" aria-labelledby=headingsavage_split data-parent=#accordionsavage_split> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#savage onclick="anchorLink('savage')">savage</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#savage_split onclick="anchorLink('savage_split')">split</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 20</span><br> <span class=description><p>Size of the batches of reads to be processed by SAVAGE. It is recommended that 500 < coverage/<code>split</code> < 1000.</p> </span> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique> <div class=card> <div class=card-header id=headinghaploclique> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique aria-expanded aria-controls=haploclique onclick="setAnchor('#haploclique')"><span class=property-name>haploclique</span></button> </h2> </div> <div id=haploclique class="collapse property-definition-div" aria-labelledby=headinghaploclique data-parent=#accordionhaploclique> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique onclick="anchorLink('haploclique')">haploclique</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionhaploclique_mem> <div class=card> <div class=card-header id=headinghaploclique_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_mem aria-expanded aria-controls=haploclique_mem onclick="setAnchor('#haploclique_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=haploclique_mem class="collapse property-definition-div" aria-labelledby=headinghaploclique_mem data-parent=#accordionhaploclique_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique onclick="anchorLink('haploclique')">haploclique</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_mem onclick="anchorLink('haploclique_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 10000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_time> <div class=card> <div class=card-header id=headinghaploclique_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_time aria-expanded aria-controls=haploclique_time onclick="setAnchor('#haploclique_time')"><span class=property-name>time</span></button> </h2> </div> <div id=haploclique_time class="collapse property-definition-div" aria-labelledby=headinghaploclique_time data-parent=#accordionhaploclique_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique onclick="anchorLink('haploclique')">haploclique</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_time onclick="anchorLink('haploclique_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1435</span><br> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_conda> <div class=card> <div class=card-header id=headinghaploclique_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_conda aria-expanded aria-controls=haploclique_conda onclick="setAnchor('#haploclique_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=haploclique_conda class="collapse property-definition-div" aria-labelledby=headinghaploclique_conda data-parent=#accordionhaploclique_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique onclick="anchorLink('haploclique')">haploclique</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_conda onclick="anchorLink('haploclique_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/haploclique.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_relax> <div class=card> <div class=card-header id=headinghaploclique_relax> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_relax aria-expanded aria-controls=haploclique_relax onclick="setAnchor('#haploclique_relax')"><span class=property-name>relax</span></button> </h2> </div> <div id=haploclique_relax class="collapse property-definition-div" aria-labelledby=headinghaploclique_relax data-parent=#accordionhaploclique_relax> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique onclick="anchorLink('haploclique')">haploclique</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_relax onclick="anchorLink('haploclique_relax')">relax</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: true</span><br> <span class=description><p>If set to <code>True</code> (default) a predefined set of parameter values is used for drawing edges between reads in the read graph.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_no_singletons> <div class=card> <div class=card-header id=headinghaploclique_no_singletons> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_no_singletons aria-expanded aria-controls=haploclique_no_singletons onclick="setAnchor('#haploclique_no_singletons')"><span class=property-name>no_singletons</span></button> </h2> </div> <div id=haploclique_no_singletons class="collapse property-definition-div" aria-labelledby=headinghaploclique_no_singletons data-parent=#accordionhaploclique_no_singletons> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique onclick="anchorLink('haploclique')">haploclique</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_no_singletons onclick="anchorLink('haploclique_no_singletons')">no_singletons</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: true</span><br> <span class=description><p>Singletons are defined as proposed haplotypes which are supported by a single read. If this property is set to <code>True</code>, singletons are discarded.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_no_prob0> <div class=card> <div class=card-header id=headinghaploclique_no_prob0> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_no_prob0 aria-expanded aria-controls=haploclique_no_prob0 onclick="setAnchor('#haploclique_no_prob0')"><span class=property-name>no_prob0</span></button> </h2> </div> <div id=haploclique_no_prob0 class="collapse property-definition-div" aria-labelledby=headinghaploclique_no_prob0 data-parent=#accordionhaploclique_no_prob0> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique onclick="anchorLink('haploclique')">haploclique</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_no_prob0 onclick="anchorLink('haploclique_no_prob0')">no_prob0</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: true</span><br> <span class=description><p>If set to <code>True</code> (default) probability of the overhangs is ignored.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_clique_size_limit> <div class=card> <div class=card-header id=headinghaploclique_clique_size_limit> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_clique_size_limit aria-expanded aria-controls=haploclique_clique_size_limit onclick="setAnchor('#haploclique_clique_size_limit')"><span class=property-name>clique_size_limit</span></button> </h2> </div> <div id=haploclique_clique_size_limit class="collapse property-definition-div" aria-labelledby=headinghaploclique_clique_size_limit data-parent=#accordionhaploclique_clique_size_limit> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique onclick="anchorLink('haploclique')">haploclique</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_clique_size_limit onclick="anchorLink('haploclique_clique_size_limit')">clique_size_limit</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 3</span><br> <span class=description><p>Sets a threshold to limit the size of cliques.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_max_num_cliques> <div class=card> <div class=card-header id=headinghaploclique_max_num_cliques> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_max_num_cliques aria-expanded aria-controls=haploclique_max_num_cliques onclick="setAnchor('#haploclique_max_num_cliques')"><span class=property-name>max_num_cliques</span></button> </h2> </div> <div id=haploclique_max_num_cliques class="collapse property-definition-div" aria-labelledby=headinghaploclique_max_num_cliques data-parent=#accordionhaploclique_max_num_cliques> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique onclick="anchorLink('haploclique')">haploclique</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_max_num_cliques onclick="anchorLink('haploclique_max_num_cliques')">max_num_cliques</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 10000</span><br> <span class=description><p>Indicates the maximum number of clique to be considered in the next iteration.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_extra_parameters> <div class=card> <div class=card-header id=headinghaploclique_extra_parameters> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_extra_parameters aria-expanded aria-controls=haploclique_extra_parameters onclick="setAnchor('#haploclique_extra_parameters')"><span class=property-name>extra_parameters</span></button> </h2> </div> <div id=haploclique_extra_parameters class="collapse property-definition-div" aria-labelledby=headinghaploclique_extra_parameters data-parent=#accordionhaploclique_extra_parameters> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique onclick="anchorLink('haploclique')">haploclique</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_extra_parameters onclick="anchorLink('haploclique_extra_parameters')">extra_parameters</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>Additional parameters to be passed to haploclique.</p> <p>Warning: this won’t overwrite the other options (e.g. <code>clique_size_limi</code> and <code>max_num_cliques</code> should still be set via their <a href=#haploclique_clique_size_limit>own</a> <a href=#haploclique_max_num_cliques>respective</a> properties, do not pass parameters <code>--limit_clique_size=</code> nor <code>--max_cliques=</code> via this <code>extra</code> property).</p> </span> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_visualization> <div class=card> <div class=card-header id=headinghaploclique_visualization> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_visualization aria-expanded aria-controls=haploclique_visualization onclick="setAnchor('#haploclique_visualization')"><span class=property-name>haploclique_visualization</span></button> </h2> </div> <div id=haploclique_visualization class="collapse property-definition-div" aria-labelledby=headinghaploclique_visualization data-parent=#accordionhaploclique_visualization> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_visualization onclick="anchorLink('haploclique_visualization')">haploclique_visualization</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionhaploclique_visualization_mem> <div class=card> <div class=card-header id=headinghaploclique_visualization_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_visualization_mem aria-expanded aria-controls=haploclique_visualization_mem onclick="setAnchor('#haploclique_visualization_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=haploclique_visualization_mem class="collapse property-definition-div" aria-labelledby=headinghaploclique_visualization_mem data-parent=#accordionhaploclique_visualization_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_visualization onclick="anchorLink('haploclique_visualization')">haploclique_visualization</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_visualization_mem onclick="anchorLink('haploclique_visualization_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 2000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_visualization_time> <div class=card> <div class=card-header id=headinghaploclique_visualization_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_visualization_time aria-expanded aria-controls=haploclique_visualization_time onclick="setAnchor('#haploclique_visualization_time')"><span class=property-name>time</span></button> </h2> </div> <div id=haploclique_visualization_time class="collapse property-definition-div" aria-labelledby=headinghaploclique_visualization_time data-parent=#accordionhaploclique_visualization_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_visualization onclick="anchorLink('haploclique_visualization')">haploclique_visualization</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_visualization_time onclick="anchorLink('haploclique_visualization_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_visualization_conda> <div class=card> <div class=card-header id=headinghaploclique_visualization_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_visualization_conda aria-expanded aria-controls=haploclique_visualization_conda onclick="setAnchor('#haploclique_visualization_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=haploclique_visualization_conda class="collapse property-definition-div" aria-labelledby=headinghaploclique_visualization_conda data-parent=#accordionhaploclique_visualization_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_visualization onclick="anchorLink('haploclique_visualization')">haploclique_visualization</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_visualization_conda onclick="anchorLink('haploclique_visualization_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/smallgenomeutilities.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_visualization_region_start> <div class=card> <div class=card-header id=headinghaploclique_visualization_region_start> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_visualization_region_start aria-expanded aria-controls=haploclique_visualization_region_start onclick="setAnchor('#haploclique_visualization_region_start')"><span class=property-name>region_start</span></button> </h2> </div> <div id=haploclique_visualization_region_start class="collapse property-definition-div" aria-labelledby=headinghaploclique_visualization_region_start data-parent=#accordionhaploclique_visualization_region_start> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_visualization onclick="anchorLink('haploclique_visualization')">haploclique_visualization</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_visualization_region_start onclick="anchorLink('haploclique_visualization_region_start')">region_start</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 0</span><br> <span class=description><p>Use to specify a region of interest.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_visualization_region_end> <div class=card> <div class=card-header id=headinghaploclique_visualization_region_end> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_visualization_region_end aria-expanded aria-controls=haploclique_visualization_region_end onclick="setAnchor('#haploclique_visualization_region_end')"><span class=property-name>region_end</span></button> </h2> </div> <div id=haploclique_visualization_region_end class="collapse property-definition-div" aria-labelledby=headinghaploclique_visualization_region_end data-parent=#accordionhaploclique_visualization_region_end> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_visualization onclick="anchorLink('haploclique_visualization')">haploclique_visualization</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_visualization_region_end onclick="anchorLink('haploclique_visualization_region_end')">region_end</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: -1</span><br> <span class=description><p>Use to specify a region of interest.</p> </span> <br> <div class="badge badge-secondary">Examples:</div> <br><div id=haploclique_visualization_region_end_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">9719</span><span class=w></span>
</pre></div> </div><div id=haploclique_visualization_region_end_ex2 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">29836</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionhaploclique_visualization_msa> <div class=card> <div class=card-header id=headinghaploclique_visualization_msa> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#haploclique_visualization_msa aria-expanded aria-controls=haploclique_visualization_msa onclick="setAnchor('#haploclique_visualization_msa')"><span class=property-name>msa</span></button> </h2> </div> <div id=haploclique_visualization_msa class="collapse property-definition-div" aria-labelledby=headinghaploclique_visualization_msa data-parent=#accordionhaploclique_visualization_msa> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_visualization onclick="anchorLink('haploclique_visualization')">haploclique_visualization</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#haploclique_visualization_msa onclick="anchorLink('haploclique_visualization_msa')">msa</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>When the ground truth is available (e.g., simulation studies), a multiple sequence alignment of types making up the population can be provided, and additional checks are performed.</p> </span> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionpredicthaplo> <div class=card> <div class=card-header id=headingpredicthaplo> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#predicthaplo aria-expanded aria-controls=predicthaplo onclick="setAnchor('#predicthaplo')"><span class=property-name>predicthaplo</span></button> </h2> </div> <div id=predicthaplo class="collapse property-definition-div" aria-labelledby=headingpredicthaplo data-parent=#accordionpredicthaplo> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#predicthaplo onclick="anchorLink('predicthaplo')">predicthaplo</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionpredicthaplo_mem> <div class=card> <div class=card-header id=headingpredicthaplo_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#predicthaplo_mem aria-expanded aria-controls=predicthaplo_mem onclick="setAnchor('#predicthaplo_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=predicthaplo_mem class="collapse property-definition-div" aria-labelledby=headingpredicthaplo_mem data-parent=#accordionpredicthaplo_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#predicthaplo onclick="anchorLink('predicthaplo')">predicthaplo</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#predicthaplo_mem onclick="anchorLink('predicthaplo_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 10000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionpredicthaplo_time> <div class=card> <div class=card-header id=headingpredicthaplo_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#predicthaplo_time aria-expanded aria-controls=predicthaplo_time onclick="setAnchor('#predicthaplo_time')"><span class=property-name>time</span></button> </h2> </div> <div id=predicthaplo_time class="collapse property-definition-div" aria-labelledby=headingpredicthaplo_time data-parent=#accordionpredicthaplo_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#predicthaplo onclick="anchorLink('predicthaplo')">predicthaplo</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#predicthaplo_time onclick="anchorLink('predicthaplo_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1435</span><br> </div> </div> </div> </div> <div class=accordion id=accordionpredicthaplo_threads> <div class=card> <div class=card-header id=headingpredicthaplo_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#predicthaplo_threads aria-expanded aria-controls=predicthaplo_threads onclick="setAnchor('#predicthaplo_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=predicthaplo_threads class="collapse property-definition-div" aria-labelledby=headingpredicthaplo_threads data-parent=#accordionpredicthaplo_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#predicthaplo onclick="anchorLink('predicthaplo')">predicthaplo</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#predicthaplo_threads onclick="anchorLink('predicthaplo_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span><br> </div> </div> </div> </div> <div class=accordion id=accordionpredicthaplo_read_min_length> <div class=card> <div class=card-header id=headingpredicthaplo_read_min_length> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#predicthaplo_read_min_length aria-expanded aria-controls=predicthaplo_read_min_length onclick="setAnchor('#predicthaplo_read_min_length')"><span class=property-name>read_min_length</span></button> </h2> </div> <div id=predicthaplo_read_min_length class="collapse property-definition-div" aria-labelledby=headingpredicthaplo_read_min_length data-parent=#accordionpredicthaplo_read_min_length> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#predicthaplo onclick="anchorLink('predicthaplo')">predicthaplo</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#predicthaplo_read_min_length onclick="anchorLink('predicthaplo_read_min_length')">read_min_length</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 0</span><br> </div> </div> </div> </div> <div class=accordion id=accordionpredicthaplo_conda> <div class=card> <div class=card-header id=headingpredicthaplo_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#predicthaplo_conda aria-expanded aria-controls=predicthaplo_conda onclick="setAnchor('#predicthaplo_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=predicthaplo_conda class="collapse property-definition-div" aria-labelledby=headingpredicthaplo_conda data-parent=#accordionpredicthaplo_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#predicthaplo onclick="anchorLink('predicthaplo')">predicthaplo</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#predicthaplo_conda onclick="anchorLink('predicthaplo_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/predicthaplo.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionamplicons> <div class=card> <div class=card-header id=headingamplicons> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#amplicons aria-expanded aria-controls=amplicons onclick="setAnchor('#amplicons')"><span class=property-name>amplicons</span></button> </h2> </div> <div id=amplicons class="collapse property-definition-div" aria-labelledby=headingamplicons data-parent=#accordionamplicons> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#amplicons onclick="anchorLink('amplicons')">amplicons</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionamplicons_mem> <div class=card> <div class=card-header id=headingamplicons_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#amplicons_mem aria-expanded aria-controls=amplicons_mem onclick="setAnchor('#amplicons_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=amplicons_mem class="collapse property-definition-div" aria-labelledby=headingamplicons_mem data-parent=#accordionamplicons_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#amplicons onclick="anchorLink('amplicons')">amplicons</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#amplicons_mem onclick="anchorLink('amplicons_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 256</span><br> </div> </div> </div> </div> <div class=accordion id=accordionamplicons_time> <div class=card> <div class=card-header id=headingamplicons_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#amplicons_time aria-expanded aria-controls=amplicons_time onclick="setAnchor('#amplicons_time')"><span class=property-name>time</span></button> </h2> </div> <div id=amplicons_time class="collapse property-definition-div" aria-labelledby=headingamplicons_time data-parent=#accordionamplicons_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#amplicons onclick="anchorLink('amplicons')">amplicons</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#amplicons_time onclick="anchorLink('amplicons_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 10</span><br> </div> </div> </div> </div> <div class=accordion id=accordionamplicons_mincooc> <div class=card> <div class=card-header id=headingamplicons_mincooc> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#amplicons_mincooc aria-expanded aria-controls=amplicons_mincooc onclick="setAnchor('#amplicons_mincooc')"><span class=property-name>mincooc</span></button> </h2> </div> <div id=amplicons_mincooc class="collapse property-definition-div" aria-labelledby=headingamplicons_mincooc data-parent=#accordionamplicons_mincooc> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#amplicons onclick="anchorLink('amplicons')">amplicons</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#amplicons_mincooc onclick="anchorLink('amplicons_mincooc')">mincooc</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 2</span><br> <span class=description><p>Minimal number of coocurrences to search for in amplicon. Lowering this property to 1 will make COJAC also look for amplicon with singleton mutations.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=amplicons_mincooc_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">1</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordioncooc> <div class=card> <div class=card-header id=headingcooc> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#cooc aria-expanded aria-controls=cooc onclick="setAnchor('#cooc')"><span class=property-name>cooc</span></button> </h2> </div> <div id=cooc class="collapse property-definition-div" aria-labelledby=headingcooc data-parent=#accordioncooc> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#cooc onclick="anchorLink('cooc')">cooc</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordioncooc_mem> <div class=card> <div class=card-header id=headingcooc_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#cooc_mem aria-expanded aria-controls=cooc_mem onclick="setAnchor('#cooc_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=cooc_mem class="collapse property-definition-div" aria-labelledby=headingcooc_mem data-parent=#accordioncooc_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#cooc onclick="anchorLink('cooc')">cooc</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#cooc_mem onclick="anchorLink('cooc_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 8192</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncooc_time> <div class=card> <div class=card-header id=headingcooc_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#cooc_time aria-expanded aria-controls=cooc_time onclick="setAnchor('#cooc_time')"><span class=property-name>time</span></button> </h2> </div> <div id=cooc_time class="collapse property-definition-div" aria-labelledby=headingcooc_time data-parent=#accordioncooc_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#cooc onclick="anchorLink('cooc')">cooc</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#cooc_time onclick="anchorLink('cooc_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 45</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncooc_threads> <div class=card> <div class=card-header id=headingcooc_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#cooc_threads aria-expanded aria-controls=cooc_threads onclick="setAnchor('#cooc_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=cooc_threads class="collapse property-definition-div" aria-labelledby=headingcooc_threads data-parent=#accordioncooc_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#cooc onclick="anchorLink('cooc')">cooc</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#cooc_threads onclick="anchorLink('cooc_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncooc_conda> <div class=card> <div class=card-header id=headingcooc_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#cooc_conda aria-expanded aria-controls=cooc_conda onclick="setAnchor('#cooc_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=cooc_conda class="collapse property-definition-div" aria-labelledby=headingcooc_conda data-parent=#accordioncooc_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#cooc onclick="anchorLink('cooc')">cooc</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#cooc_conda onclick="anchorLink('cooc_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/cojac.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordioncooc_out_format> <div class=card> <div class=card-header id=headingcooc_out_format> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#cooc_out_format aria-expanded aria-controls=cooc_out_format onclick="setAnchor('#cooc_out_format')"><span class=property-name>out_format</span></button> </h2> </div> <div id=cooc_out_format class="collapse property-definition-div" aria-labelledby=headingcooc_out_format data-parent=#accordioncooc_out_format> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#cooc onclick="anchorLink('cooc')">cooc</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#cooc_out_format onclick="anchorLink('cooc_out_format')">out_format</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "lines"</span><br> <span class=description><p>Format of the output CSV.</p> <ul> <li><code>lines</code>(default) - each amplicon a separate entry on a separate line.</li> <li><code>columns</code> - one column per amplicon</li> </ul> </span><div class=enum-value id=cooc_out_format_enum> <h4>Must be one of:</h4> <ul class=list-group><li class="list-group-item enum-item">"lines"</li><li class="list-group-item enum-item">"columns"</li></ul> </div> <br> <div class="badge badge-secondary">Example:</div> <br><div id=cooc_out_format_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">columns</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionmutlist> <div class=card> <div class=card-header id=headingmutlist> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#mutlist aria-expanded aria-controls=mutlist onclick="setAnchor('#mutlist')"><span class=property-name>mutlist</span></button> </h2> </div> <div id=mutlist class="collapse property-definition-div" aria-labelledby=headingmutlist data-parent=#accordionmutlist> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#mutlist onclick="anchorLink('mutlist')">mutlist</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionmutlist_mem> <div class=card> <div class=card-header id=headingmutlist_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#mutlist_mem aria-expanded aria-controls=mutlist_mem onclick="setAnchor('#mutlist_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=mutlist_mem class="collapse property-definition-div" aria-labelledby=headingmutlist_mem data-parent=#accordionmutlist_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#mutlist onclick="anchorLink('mutlist')">mutlist</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#mutlist_mem onclick="anchorLink('mutlist_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 256</span><br> </div> </div> </div> </div> <div class=accordion id=accordionmutlist_time> <div class=card> <div class=card-header id=headingmutlist_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#mutlist_time aria-expanded aria-controls=mutlist_time onclick="setAnchor('#mutlist_time')"><span class=property-name>time</span></button> </h2> </div> <div id=mutlist_time class="collapse property-definition-div" aria-labelledby=headingmutlist_time data-parent=#accordionmutlist_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#mutlist onclick="anchorLink('mutlist')">mutlist</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#mutlist_time onclick="anchorLink('mutlist_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 10</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionsigmut> <div class=card> <div class=card-header id=headingsigmut> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#sigmut aria-expanded aria-controls=sigmut onclick="setAnchor('#sigmut')"><span class=property-name>sigmut</span></button> </h2> </div> <div id=sigmut class="collapse property-definition-div" aria-labelledby=headingsigmut data-parent=#accordionsigmut> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#sigmut onclick="anchorLink('sigmut')">sigmut</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionsigmut_mem> <div class=card> <div class=card-header id=headingsigmut_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#sigmut_mem aria-expanded aria-controls=sigmut_mem onclick="setAnchor('#sigmut_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=sigmut_mem class="collapse property-definition-div" aria-labelledby=headingsigmut_mem data-parent=#accordionsigmut_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#sigmut onclick="anchorLink('sigmut')">sigmut</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#sigmut_mem onclick="anchorLink('sigmut_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 4096</span><br> </div> </div> </div> </div> <div class=accordion id=accordionsigmut_time> <div class=card> <div class=card-header id=headingsigmut_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#sigmut_time aria-expanded aria-controls=sigmut_time onclick="setAnchor('#sigmut_time')"><span class=property-name>time</span></button> </h2> </div> <div id=sigmut_time class="collapse property-definition-div" aria-labelledby=headingsigmut_time data-parent=#accordionsigmut_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#sigmut onclick="anchorLink('sigmut')">sigmut</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#sigmut_time onclick="anchorLink('sigmut_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 15</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordiontimeline> <div class=card> <div class=card-header id=headingtimeline> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#timeline aria-expanded aria-controls=timeline onclick="setAnchor('#timeline')"><span class=property-name>timeline</span></button> </h2> </div> <div id=timeline class="collapse property-definition-div" aria-labelledby=headingtimeline data-parent=#accordiontimeline> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline onclick="anchorLink('timeline')">timeline</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <span class=description><p>This section is used to set up a timeline of the samples. Some output, e.g., deconvolution of quasispecies mixture using LolliPop, need to have a time component. By default it calls a script that uses regular expressions and look-up tables to extract this information from the samples’ own names. But by using the properties <code>script</code> and <code>options</code> and adapting the environment provided in property <code>conda</code>, it is possible to heavily customize the actions (e.g. it is possible to query an external database instead). For inspiration, see the default script <code>file_parser.py</code>.</p> </span> <div class=accordion id=accordiontimeline_mem> <div class=card> <div class=card-header id=headingtimeline_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#timeline_mem aria-expanded aria-controls=timeline_mem onclick="setAnchor('#timeline_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=timeline_mem class="collapse property-definition-div" aria-labelledby=headingtimeline_mem data-parent=#accordiontimeline_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline onclick="anchorLink('timeline')">timeline</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline_mem onclick="anchorLink('timeline_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1024</span><br> </div> </div> </div> </div> <div class=accordion id=accordiontimeline_time> <div class=card> <div class=card-header id=headingtimeline_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#timeline_time aria-expanded aria-controls=timeline_time onclick="setAnchor('#timeline_time')"><span class=property-name>time</span></button> </h2> </div> <div id=timeline_time class="collapse property-definition-div" aria-labelledby=headingtimeline_time data-parent=#accordiontimeline_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline onclick="anchorLink('timeline')">timeline</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline_time onclick="anchorLink('timeline_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 15</span><br> </div> </div> </div> </div> <div class=accordion id=accordiontimeline_conda> <div class=card> <div class=card-header id=headingtimeline_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#timeline_conda aria-expanded aria-controls=timeline_conda onclick="setAnchor('#timeline_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=timeline_conda class="collapse property-definition-div" aria-labelledby=headingtimeline_conda data-parent=#accordiontimeline_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline onclick="anchorLink('timeline')">timeline</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline_conda onclick="anchorLink('timeline_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/timeline.yaml"</span><br> <span class=description><p>The default environment only provides regular expression functions (<code>python-reges</code>) but depending on your needs you would want to provide a custom environment with additional tools (e.g. drivers to query a databse, etc.)</p> </span> </div> </div> </div> </div> <div class=accordion id=accordiontimeline_threads> <div class=card> <div class=card-header id=headingtimeline_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#timeline_threads aria-expanded aria-controls=timeline_threads onclick="setAnchor('#timeline_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=timeline_threads class="collapse property-definition-div" aria-labelledby=headingtimeline_threads data-parent=#accordiontimeline_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline onclick="anchorLink('timeline')">timeline</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline_threads onclick="anchorLink('timeline_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1</span><br> </div> </div> </div> </div> <div class=accordion id=accordiontimeline_local> <div class=card> <div class=card-header id=headingtimeline_local> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#timeline_local aria-expanded aria-controls=timeline_local onclick="setAnchor('#timeline_local')"><span class=property-name>local</span></button> </h2> </div> <div id=timeline_local class="collapse property-definition-div" aria-labelledby=headingtimeline_local data-parent=#accordiontimeline_local> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline onclick="anchorLink('timeline')">timeline</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline_local onclick="anchorLink('timeline_local')">local</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: true</span><br> <span class=description><p>Don’t dispatch the timeline rule to the cluster for execution, run locally.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=timeline_local_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">False</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiontimeline_script> <div class=card> <div class=card-header id=headingtimeline_script> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#timeline_script aria-expanded aria-controls=timeline_script onclick="setAnchor('#timeline_script')"><span class=property-name>script</span></button> </h2> </div> <div id=timeline_script class="collapse property-definition-div" aria-labelledby=headingtimeline_script data-parent=#accordiontimeline_script> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline onclick="anchorLink('timeline')">timeline</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline_script onclick="anchorLink('timeline_script')">script</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/scripts/file_parser.py"</span><br> <span class=description><p>Script that sets up a timeline of the samples.</p> <p>Its purpose is to take the V-pipe’s samples TSV file and add two columns:</p> <ul> <li><em>location</em>: location of the sampes</li> <li><em>date</em>: sampling date of the samples</li> </ul> <p>It will receive the following parameters (in addition to what is specified in property <em>options</em>:</p> <ul> <li><em>–output <OUTPUT></em>: the output TSV file that must be created by the script.</li> <li><em><SAMPLE_TSV></em>: the input samples TSV file</li> </ul> <p>For an example, see the default script <code>file_parser.py</code>, it uses regular expressions (regex) to parse the first two columns (sample and batch names) and extract a date, and a location code that is further look-ed up in a table. It takes two additional parameters:</p> <ul> <li><em>–locations <LOOKUP></em>: look-up TSV table mapping the code to full location names</li> <li><em>–regex_yaml <YAML></em>: YAML file with regular expressions defining how the date and code are extracted.</li> </ul> </span> </div> </div> </div> </div> <div class=accordion id=accordiontimeline_options> <div class=card> <div class=card-header id=headingtimeline_options> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#timeline_options aria-expanded aria-controls=timeline_options onclick="setAnchor('#timeline_options')"><span class=property-name>options</span></button> </h2> </div> <div id=timeline_options class="collapse property-definition-div" aria-labelledby=headingtimeline_options data-parent=#accordiontimeline_options> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline onclick="anchorLink('timeline')">timeline</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline_options onclick="anchorLink('timeline_options')">options</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: " --no-fallback"</span><br> <span class=description><p>Additional options to be passed to the script, e.g. for an extra configuration file with database server information.</p> <p>By default, passes an option to the default script to force always using the regex (do not fall back to copy-pasting columns).</p> </span> </div> </div> </div> </div> <div class=accordion id=accordiontimeline_locations_table> <div class=card> <div class=card-header id=headingtimeline_locations_table> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#timeline_locations_table aria-expanded aria-controls=timeline_locations_table onclick="setAnchor('#timeline_locations_table')"><span class=property-name>locations_table</span></button> </h2> </div> <div id=timeline_locations_table class="collapse property-definition-div" aria-labelledby=headingtimeline_locations_table data-parent=#accordiontimeline_locations_table> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline onclick="anchorLink('timeline')">timeline</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline_locations_table onclick="anchorLink('timeline_locations_table')">locations_table</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>Option for the default script: TSV table that maps location codes (e.g. short alphanumeric codes) used in sample names to full names of locations (e.g. city names).</p> <p>For example:</p> <pre><code>code location
10 Zürich (ZH)
16 Genève (GE)
Ba Basel (BS)
</code></pre> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=timeline_locations_table_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">wastewater_plants.tsv</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiontimeline_regex_yaml> <div class=card> <div class=card-header id=headingtimeline_regex_yaml> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#timeline_regex_yaml aria-expanded aria-controls=timeline_regex_yaml onclick="setAnchor('#timeline_regex_yaml')"><span class=property-name>regex_yaml</span></button> </h2> </div> <div id=timeline_regex_yaml class="collapse property-definition-div" aria-labelledby=headingtimeline_regex_yaml data-parent=#accordiontimeline_regex_yaml> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline onclick="anchorLink('timeline')">timeline</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#timeline_regex_yaml onclick="anchorLink('timeline_regex_yaml')">regex_yaml</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>Option for the default script: YAML file the defines how to parse time series information out of the columns of <em>samples.tsv</em>, e.g.:</p> <div class="highlight jumbotron"><pre><span></span><code><span class=nt>sample</span><span class=p>:</span><span class=w> </span><span class="l l-Scalar l-Scalar-Plain">(?P<location>\d+)_(?P<year>20\d{2})_(?P<month>[01]?\d)_(?P<day>[0-3]?\d)</span><span class=w></span>
<span class=nt>datefmt</span><span class=p>:</span><span class=w> </span><span class=s>"%Y%m%d"</span><span class=w></span>
</code></pre></div> <ul> <li>by default, <em>samples.tsv</em>’s first column (sample names) is used as-is for location codes and the second column (sequencing batch dates) is used for timeline’s date point.</li> <li>YAML’s optional entry <code>sample</code> defines a regular expression to be applied on the first column (sample names)</li> <li>YAML’s optional entry <code>batch</code> defines a regular expression to be applied on the second column (sequencing batch dates)</li> <li>regular expression <strong>must</strong> define the following <a href=https://www.regular-expressions.info/named.html>named capturing groups</a>:<br> <ul><br> <li><code>location</code> used for the location codes</li><br> <li><code>year</code>, <code>month</code>, <code>day</code> used for the dates of the timeline</li><br> <li>alternatively, if the date doesn’t use a format with <em>year + month + day</em> elements – e.g., date uses week number of the year – group <code>date</code> can be used to capture the whole date string</li><br> </ul></li> <li>YAML’s optional entry <code>datefmt</code> gives a <a href=https://docs.python.org/3/library/time.html#time.strftime>time format string</a> to parse the <code>date</code> capturing group.</li> </ul> </span> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordiontallymut> <div class=card> <div class=card-header id=headingtallymut> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#tallymut aria-expanded aria-controls=tallymut onclick="setAnchor('#tallymut')"><span class=property-name>tallymut</span></button> </h2> </div> <div id=tallymut class="collapse property-definition-div" aria-labelledby=headingtallymut data-parent=#accordiontallymut> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#tallymut onclick="anchorLink('tallymut')">tallymut</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordiontallymut_mem> <div class=card> <div class=card-header id=headingtallymut_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#tallymut_mem aria-expanded aria-controls=tallymut_mem onclick="setAnchor('#tallymut_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=tallymut_mem class="collapse property-definition-div" aria-labelledby=headingtallymut_mem data-parent=#accordiontallymut_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#tallymut onclick="anchorLink('tallymut')">tallymut</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#tallymut_mem onclick="anchorLink('tallymut_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 4096</span><br> </div> </div> </div> </div> <div class=accordion id=accordiontallymut_time> <div class=card> <div class=card-header id=headingtallymut_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#tallymut_time aria-expanded aria-controls=tallymut_time onclick="setAnchor('#tallymut_time')"><span class=property-name>time</span></button> </h2> </div> <div id=tallymut_time class="collapse property-definition-div" aria-labelledby=headingtallymut_time data-parent=#accordiontallymut_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#tallymut onclick="anchorLink('tallymut')">tallymut</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#tallymut_time onclick="anchorLink('tallymut_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 30</span><br> </div> </div> </div> </div> <div class=accordion id=accordiontallymut_conda> <div class=card> <div class=card-header id=headingtallymut_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#tallymut_conda aria-expanded aria-controls=tallymut_conda onclick="setAnchor('#tallymut_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=tallymut_conda class="collapse property-definition-div" aria-labelledby=headingtallymut_conda data-parent=#accordiontallymut_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#tallymut onclick="anchorLink('tallymut')">tallymut</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#tallymut_conda onclick="anchorLink('tallymut_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/xsv.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordiontallymut_timeline_file> <div class=card> <div class=card-header id=headingtallymut_timeline_file> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#tallymut_timeline_file aria-expanded aria-controls=tallymut_timeline_file onclick="setAnchor('#tallymut_timeline_file')"><span class=property-name>timeline_file</span></button> </h2> </div> <div id=tallymut_timeline_file class="collapse property-definition-div" aria-labelledby=headingtallymut_timeline_file data-parent=#accordiontallymut_timeline_file> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#tallymut onclick="anchorLink('tallymut')">tallymut</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#tallymut_timeline_file onclick="anchorLink('tallymut_timeline_file')">timeline_file</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>If set, this user-provided TSV file (e.g.: generated with an external tool, prior of running V-pipe) will be used for obtaining locations and dates – as needed by LolliPop – instead of generating <code>results/timeline.tsv</code> with the rule timeline.<br> This follows the following format (similar to the output of rule timeline):</p> <pre><code>sample batch reads proto location_code date location
A1_05_2023_04_12 20230428_HNG5MDRX2 250 v41 5 2023-04-12 Lugano (TI)
A2_10_2023_04_13 20230428_HNG5MDRX2 250 v41 10 2023-04-13 Zürich (ZH)
A3_16_2023_04_14 20230428_HNG5MDRX2 250 v41 16 2023-04-14 Genève (GE)
…
</code></pre> <ul> <li>The extra columns <em>location</em> and <em>data</em> are <strong>necessary</strong> for LolliPop.</li> <li>Columns <em>sample</em>, <em>batch</em>, <em>reads</em> and <em>proto</em> are simply the fist four columns of <code>samples.tsv</code><br> <ul><br> <li>V-pipe only needs column <em>sample</em> and <em>batch</em> for now.</li><br> </ul></li> </ul> </span> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordiondeconvolution> <div class=card> <div class=card-header id=headingdeconvolution> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#deconvolution aria-expanded aria-controls=deconvolution onclick="setAnchor('#deconvolution')"><span class=property-name>deconvolution</span></button> </h2> </div> <div id=deconvolution class="collapse property-definition-div" aria-labelledby=headingdeconvolution data-parent=#accordiondeconvolution> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution onclick="anchorLink('deconvolution')">deconvolution</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordiondeconvolution_mem> <div class=card> <div class=card-header id=headingdeconvolution_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#deconvolution_mem aria-expanded aria-controls=deconvolution_mem onclick="setAnchor('#deconvolution_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=deconvolution_mem class="collapse property-definition-div" aria-labelledby=headingdeconvolution_mem data-parent=#accordiondeconvolution_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution onclick="anchorLink('deconvolution')">deconvolution</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution_mem onclick="anchorLink('deconvolution_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 4096</span><br> </div> </div> </div> </div> <div class=accordion id=accordiondeconvolution_time> <div class=card> <div class=card-header id=headingdeconvolution_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#deconvolution_time aria-expanded aria-controls=deconvolution_time onclick="setAnchor('#deconvolution_time')"><span class=property-name>time</span></button> </h2> </div> <div id=deconvolution_time class="collapse property-definition-div" aria-labelledby=headingdeconvolution_time data-parent=#accordiondeconvolution_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution onclick="anchorLink('deconvolution')">deconvolution</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution_time onclick="anchorLink('deconvolution_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 240</span><br> </div> </div> </div> </div> <div class=accordion id=accordiondeconvolution_threads> <div class=card> <div class=card-header id=headingdeconvolution_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#deconvolution_threads aria-expanded aria-controls=deconvolution_threads onclick="setAnchor('#deconvolution_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=deconvolution_threads class="collapse property-definition-div" aria-labelledby=headingdeconvolution_threads data-parent=#accordiondeconvolution_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution onclick="anchorLink('deconvolution')">deconvolution</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution_threads onclick="anchorLink('deconvolution_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 4</span><br> </div> </div> </div> </div> <div class=accordion id=accordiondeconvolution_conda> <div class=card> <div class=card-header id=headingdeconvolution_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#deconvolution_conda aria-expanded aria-controls=deconvolution_conda onclick="setAnchor('#deconvolution_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=deconvolution_conda class="collapse property-definition-div" aria-labelledby=headingdeconvolution_conda data-parent=#accordiondeconvolution_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution onclick="anchorLink('deconvolution')">deconvolution</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution_conda onclick="anchorLink('deconvolution_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/lollipop.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordiondeconvolution_deconvolution_config> <div class=card> <div class=card-header id=headingdeconvolution_deconvolution_config> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#deconvolution_deconvolution_config aria-expanded aria-controls=deconvolution_deconvolution_config onclick="setAnchor('#deconvolution_deconvolution_config')"><span class=property-name>deconvolution_config</span></button> </h2> </div> <div id=deconvolution_deconvolution_config class="collapse property-definition-div" aria-labelledby=headingdeconvolution_deconvolution_config data-parent=#accordiondeconvolution_deconvolution_config> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution onclick="anchorLink('deconvolution')">deconvolution</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution_deconvolution_config onclick="anchorLink('deconvolution_deconvolution_config')">deconvolution_config</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/../resources/cowwid/deconv_linear_logit_quasi_strat.yaml"</span><br> <span class=description><p>Configuration file with parameters for kernel deconvolution</p> </span> <br> <div class="badge badge-secondary">Examples:</div> <br><div id=deconvolution_deconvolution_config_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">/git/lollipop/deconv_linear_logit_quasi_strat.yaml</span><span class=w></span>
</pre></div> </div><div id=deconvolution_deconvolution_config_ex2 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">/git/lollipop/deconv_linear_wald.yaml</span><span class=w></span>
</pre></div> </div><div id=deconvolution_deconvolution_config_ex3 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">/git/lollipop/deconv_bootstrap</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiondeconvolution_variants_config> <div class=card> <div class=card-header id=headingdeconvolution_variants_config> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#deconvolution_variants_config aria-expanded aria-controls=deconvolution_variants_config onclick="setAnchor('#deconvolution_variants_config')"><span class=property-name>variants_config</span></button> </h2> </div> <div id=deconvolution_variants_config class="collapse property-definition-div" aria-labelledby=headingdeconvolution_variants_config data-parent=#accordiondeconvolution_variants_config> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution onclick="anchorLink('deconvolution')">deconvolution</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution_variants_config onclick="anchorLink('deconvolution_variants_config')">variants_config</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>Variants configuration used during deconvolution</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=deconvolution_variants_config_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">var_conf.yaml</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiondeconvolution_variants_dates> <div class=card> <div class=card-header id=headingdeconvolution_variants_dates> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#deconvolution_variants_dates aria-expanded aria-controls=deconvolution_variants_dates onclick="setAnchor('#deconvolution_variants_dates')"><span class=property-name>variants_dates</span></button> </h2> </div> <div id=deconvolution_variants_dates class="collapse property-definition-div" aria-labelledby=headingdeconvolution_variants_dates data-parent=#accordiondeconvolution_variants_dates> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution onclick="anchorLink('deconvolution')">deconvolution</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution_variants_dates onclick="anchorLink('deconvolution_variants_dates')">variants_dates</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>Variants to scan per periods (as determined with COJAC by leveraging the output of the cooc rule)</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=deconvolution_variants_dates_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">var_dates.yaml</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiondeconvolution_out_format> <div class=card> <div class=card-header id=headingdeconvolution_out_format> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#deconvolution_out_format aria-expanded aria-controls=deconvolution_out_format onclick="setAnchor('#deconvolution_out_format')"><span class=property-name>out_format</span></button> </h2> </div> <div id=deconvolution_out_format class="collapse property-definition-div" aria-labelledby=headingdeconvolution_out_format data-parent=#accordiondeconvolution_out_format> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution onclick="anchorLink('deconvolution')">deconvolution</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution_out_format onclick="anchorLink('deconvolution_out_format')">out_format</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "lines"</span><br> <span class=description><p>Format of the output CSV.</p> <ul> <li><code>lines</code>(default) - each variants a separate entry on a separate line.</li> <li><code>columns</code> - one column per variant</li> </ul> </span><div class=enum-value id=deconvolution_out_format_enum> <h4>Must be one of:</h4> <ul class=list-group><li class="list-group-item enum-item">"lines"</li><li class="list-group-item enum-item">"columns"</li></ul> </div> <br> <div class="badge badge-secondary">Example:</div> <br><div id=deconvolution_out_format_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">columns</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiondeconvolution_filters> <div class=card> <div class=card-header id=headingdeconvolution_filters> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#deconvolution_filters aria-expanded aria-controls=deconvolution_filters onclick="setAnchor('#deconvolution_filters')"><span class=property-name>filters</span></button> </h2> </div> <div id=deconvolution_filters class="collapse property-definition-div" aria-labelledby=headingdeconvolution_filters data-parent=#accordiondeconvolution_filters> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution onclick="anchorLink('deconvolution')">deconvolution</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#deconvolution_filters onclick="anchorLink('deconvolution_filters')">filters</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>List of filters for removing problematic mutations from tally. Some mutations might be problematic and need to be taken out – e.g. due to drop-outs in the multiplex PCR amplification, they do not show up in the data and this could be misinterpreted by LolliPop as proof of absence of a variant.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=deconvolution_filters_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">filters_preprint.yaml</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionweb_visualization> <div class=card> <div class=card-header id=headingweb_visualization> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#web_visualization aria-expanded aria-controls=web_visualization onclick="setAnchor('#web_visualization')"><span class=property-name>web_visualization</span></button> </h2> </div> <div id=web_visualization class="collapse property-definition-div" aria-labelledby=headingweb_visualization data-parent=#accordionweb_visualization> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#web_visualization onclick="anchorLink('web_visualization')">web_visualization</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionweb_visualization_mem> <div class=card> <div class=card-header id=headingweb_visualization_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#web_visualization_mem aria-expanded aria-controls=web_visualization_mem onclick="setAnchor('#web_visualization_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=web_visualization_mem class="collapse property-definition-div" aria-labelledby=headingweb_visualization_mem data-parent=#accordionweb_visualization_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#web_visualization onclick="anchorLink('web_visualization')">web_visualization</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#web_visualization_mem onclick="anchorLink('web_visualization_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 2000</span><br> </div> </div> </div> </div> <div class=accordion id=accordionweb_visualization_time> <div class=card> <div class=card-header id=headingweb_visualization_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#web_visualization_time aria-expanded aria-controls=web_visualization_time onclick="setAnchor('#web_visualization_time')"><span class=property-name>time</span></button> </h2> </div> <div id=web_visualization_time class="collapse property-definition-div" aria-labelledby=headingweb_visualization_time data-parent=#accordionweb_visualization_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#web_visualization onclick="anchorLink('web_visualization')">web_visualization</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#web_visualization_time onclick="anchorLink('web_visualization_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordionweb_visualization_conda> <div class=card> <div class=card-header id=headingweb_visualization_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#web_visualization_conda aria-expanded aria-controls=web_visualization_conda onclick="setAnchor('#web_visualization_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=web_visualization_conda class="collapse property-definition-div" aria-labelledby=headingweb_visualization_conda data-parent=#accordionweb_visualization_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#web_visualization onclick="anchorLink('web_visualization')">web_visualization</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#web_visualization_conda onclick="anchorLink('web_visualization_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/visualization.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordiondiversity> <div class=card> <div class=card-header id=headingdiversity> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#diversity aria-expanded aria-controls=diversity onclick="setAnchor('#diversity')"><span class=property-name>diversity</span></button> </h2> </div> <div id=diversity class="collapse property-definition-div" aria-labelledby=headingdiversity data-parent=#accordiondiversity> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#diversity onclick="anchorLink('diversity')">diversity</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordiondiversity_mem> <div class=card> <div class=card-header id=headingdiversity_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#diversity_mem aria-expanded aria-controls=diversity_mem onclick="setAnchor('#diversity_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=diversity_mem class="collapse property-definition-div" aria-labelledby=headingdiversity_mem data-parent=#accordiondiversity_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#diversity onclick="anchorLink('diversity')">diversity</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#diversity_mem onclick="anchorLink('diversity_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 2000</span><br> </div> </div> </div> </div> <div class=accordion id=accordiondiversity_time> <div class=card> <div class=card-header id=headingdiversity_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#diversity_time aria-expanded aria-controls=diversity_time onclick="setAnchor('#diversity_time')"><span class=property-name>time</span></button> </h2> </div> <div id=diversity_time class="collapse property-definition-div" aria-labelledby=headingdiversity_time data-parent=#accordiondiversity_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#diversity onclick="anchorLink('diversity')">diversity</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#diversity_time onclick="anchorLink('diversity_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordiondiversity_conda> <div class=card> <div class=card-header id=headingdiversity_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#diversity_conda aria-expanded aria-controls=diversity_conda onclick="setAnchor('#diversity_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=diversity_conda class="collapse property-definition-div" aria-labelledby=headingdiversity_conda data-parent=#accordiondiversity_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#diversity onclick="anchorLink('diversity')">diversity</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#diversity_conda onclick="anchorLink('diversity_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/diversity_measures.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordiondehuman> <div class=card> <div class=card-header id=headingdehuman> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#dehuman aria-expanded aria-controls=dehuman onclick="setAnchor('#dehuman')"><span class=property-name>dehuman</span></button> </h2> </div> <div id=dehuman class="collapse property-definition-div" aria-labelledby=headingdehuman data-parent=#accordiondehuman> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman onclick="anchorLink('dehuman')">dehuman</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordiondehuman_conda> <div class=card> <div class=card-header id=headingdehuman_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#dehuman_conda aria-expanded aria-controls=dehuman_conda onclick="setAnchor('#dehuman_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=dehuman_conda class="collapse property-definition-div" aria-labelledby=headingdehuman_conda data-parent=#accordiondehuman_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman onclick="anchorLink('dehuman')">dehuman</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman_conda onclick="anchorLink('dehuman_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/dehuman.yaml"</span><br> </div> </div> </div> </div> <div class=accordion id=accordiondehuman_mem> <div class=card> <div class=card-header id=headingdehuman_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#dehuman_mem aria-expanded aria-controls=dehuman_mem onclick="setAnchor('#dehuman_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=dehuman_mem class="collapse property-definition-div" aria-labelledby=headingdehuman_mem data-parent=#accordiondehuman_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman onclick="anchorLink('dehuman')">dehuman</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman_mem onclick="anchorLink('dehuman_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 4096</span><br> </div> </div> </div> </div> <div class=accordion id=accordiondehuman_time> <div class=card> <div class=card-header id=headingdehuman_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#dehuman_time aria-expanded aria-controls=dehuman_time onclick="setAnchor('#dehuman_time')"><span class=property-name>time</span></button> </h2> </div> <div id=dehuman_time class="collapse property-definition-div" aria-labelledby=headingdehuman_time data-parent=#accordiondehuman_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman onclick="anchorLink('dehuman')">dehuman</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman_time onclick="anchorLink('dehuman_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 235</span><br> </div> </div> </div> </div> <div class=accordion id=accordiondehuman_threads> <div class=card> <div class=card-header id=headingdehuman_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#dehuman_threads aria-expanded aria-controls=dehuman_threads onclick="setAnchor('#dehuman_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=dehuman_threads class="collapse property-definition-div" aria-labelledby=headingdehuman_threads data-parent=#accordiondehuman_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman onclick="anchorLink('dehuman')">dehuman</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman_threads onclick="anchorLink('dehuman_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 4</span><br> </div> </div> </div> </div> <div class=accordion id=accordiondehuman_ref_host> <div class=card> <div class=card-header id=headingdehuman_ref_host> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#dehuman_ref_host aria-expanded aria-controls=dehuman_ref_host onclick="setAnchor('#dehuman_ref_host')"><span class=property-name>ref_host</span></button> </h2> </div> <div id=dehuman_ref_host class="collapse property-definition-div" aria-labelledby=headingdehuman_ref_host data-parent=#accordiondehuman_ref_host> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman onclick="anchorLink('dehuman')">dehuman</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman_ref_host onclick="anchorLink('dehuman_ref_host')">ref_host</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "references/human.fa.gz"</span><br> <span class=description><p>Host’s genome used to remove reads (e.g. human genome)</p> <p><strong>Note:</strong> if this file is absent, it is possible to fetch it from a remote server, see property <code>ref_host_url</code> below.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=dehuman_ref_host_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">/cluster/project/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiondehuman_ref_host_url> <div class=card> <div class=card-header id=headingdehuman_ref_host_url> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#dehuman_ref_host_url aria-expanded aria-controls=dehuman_ref_host_url onclick="setAnchor('#dehuman_ref_host_url')"><span class=property-name>ref_host_url</span></button> </h2> </div> <div id=dehuman_ref_host_url class="collapse property-definition-div" aria-labelledby=headingdehuman_ref_host_url data-parent=#accordiondehuman_ref_host_url> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman onclick="anchorLink('dehuman')">dehuman</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman_ref_host_url onclick="anchorLink('dehuman_ref_host_url')">ref_host_url</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "http://ftp.ensembl.org/pub/current_fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"</span><br> <span class=description><p>If the host’s genome specified in property <code>ref_host</code> isn’t present, fetch it from a remote server.</p> <p><strong>Note</strong> remember to set aside enough memory for the indexing rule, see section <code>ref_bwa_index</code> property <code>mem</code>.</p> </span> <br> <div class="badge badge-secondary">Examples:</div> <br><div id=dehuman_ref_host_url_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">http://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz</span><span class=w></span>
</pre></div> </div><div id=dehuman_ref_host_url_ex2 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.29_GRCh38.p14/GCA_000001405.29_GRCh38.p14_genomic.fna.gz</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiondehuman_keep_host> <div class=card> <div class=card-header id=headingdehuman_keep_host> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#dehuman_keep_host aria-expanded aria-controls=dehuman_keep_host onclick="setAnchor('#dehuman_keep_host')"><span class=property-name>keep_host</span></button> </h2> </div> <div id=dehuman_keep_host class="collapse property-definition-div" aria-labelledby=headingdehuman_keep_host data-parent=#accordiondehuman_keep_host> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman onclick="anchorLink('dehuman')">dehuman</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman_keep_host onclick="anchorLink('dehuman_keep_host')">keep_host</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>Indicate whether to store the host-aligned reads in a CRAM file <code>…/alignments/host_aln.cram</code>.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=dehuman_keep_host_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordiondehuman_catchup> <div class=card> <div class=card-header id=headingdehuman_catchup> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#dehuman_catchup aria-expanded aria-controls=dehuman_catchup onclick="setAnchor('#dehuman_catchup')"><span class=property-name>catchup</span></button> </h2> </div> <div id=dehuman_catchup class="collapse property-definition-div" aria-labelledby=headingdehuman_catchup data-parent=#accordiondehuman_catchup> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman onclick="anchorLink('dehuman')">dehuman</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#dehuman_catchup onclick="anchorLink('dehuman_catchup')">catchup</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>Use this option when generating dehumanized raw reads (<code>dehuman.cram</code>) on old samples <em><strong>that have already</strong></em> been processed in the past — a <em>catch up</em>.</p> <p>Normally, removing host-mapping reads requires analyzing reads which were rejected by V-pipe’s main processing (as specified in section <code>general</code>, property <code>aligner</code>). But this output is considered temporary and will get deleted by Snakemake once the processing of a sample has finished. To generate <code>dehuman.cram</code> V-pipe would need to run the aligner again, which will both regenerate the data necessary for this output but also generate a new alignment which will trigger the whole workflow again.<br> Use this property <code>catchup</code> to only generate the input necessary for <code>dehuman.cram</code>, leaving untouched the alignment and everything else that has already been processed.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=dehuman_catchup_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionchecksum> <div class=card> <div class=card-header id=headingchecksum> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#checksum aria-expanded aria-controls=checksum onclick="setAnchor('#checksum')"><span class=property-name>checksum</span></button> </h2> </div> <div id=checksum class="collapse property-definition-div" aria-labelledby=headingchecksum data-parent=#accordionchecksum> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#checksum onclick="anchorLink('checksum')">checksum</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <div class=accordion id=accordionchecksum_mem> <div class=card> <div class=card-header id=headingchecksum_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#checksum_mem aria-expanded aria-controls=checksum_mem onclick="setAnchor('#checksum_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=checksum_mem class="collapse property-definition-div" aria-labelledby=headingchecksum_mem data-parent=#accordionchecksum_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#checksum onclick="anchorLink('checksum')">checksum</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#checksum_mem onclick="anchorLink('checksum_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 256</span><br> </div> </div> </div> </div> <div class=accordion id=accordionchecksum_time> <div class=card> <div class=card-header id=headingchecksum_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#checksum_time aria-expanded aria-controls=checksum_time onclick="setAnchor('#checksum_time')"><span class=property-name>time</span></button> </h2> </div> <div id=checksum_time class="collapse property-definition-div" aria-labelledby=headingchecksum_time data-parent=#accordionchecksum_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#checksum onclick="anchorLink('checksum')">checksum</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#checksum_time onclick="anchorLink('checksum_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 60</span><br> </div> </div> </div> </div> <div class=accordion id=accordionchecksum_conda> <div class=card> <div class=card-header id=headingchecksum_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#checksum_conda aria-expanded aria-controls=checksum_conda onclick="setAnchor('#checksum_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=checksum_conda class="collapse property-definition-div" aria-labelledby=headingchecksum_conda data-parent=#accordionchecksum_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#checksum onclick="anchorLink('checksum')">checksum</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#checksum_conda onclick="anchorLink('checksum_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/upload.yaml"</span><br> </div> </div> </div> </div> </div> </div> </div> </div> <div class=accordion id=accordionupload> <div class=card> <div class=card-header id=headingupload> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#upload aria-expanded aria-controls=upload onclick="setAnchor('#upload')"><span class=property-name>upload</span></button> </h2> </div> <div id=upload class="collapse property-definition-div" aria-labelledby=headingupload data-parent=#accordionupload> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload onclick="anchorLink('upload')">upload</a></div><span class="badge badge-dark value-type">Type: object</span> <span class="badge badge-success default-value">Default: {}</span><br> <span class=description><p>This section is used to assist and prepare uploads of the data, e.g. to European Nucleotide Archive. By default it calls a script that creates symlinks making it easy to identify new/updated samples between calls of V-pipe. But by using the properties <code>script</code> and <code>options</code> and adapting the environment provided in property <code>conda</code>, it is possible to heavily customize the actions (e.g. it is possible to upload to an SFTP server by calling <code>sftp</code> from a modified script). For inspiration, see the default script <code>prepare_upload_symlinks.sh</code>.</p> </span> <div class=accordion id=accordionupload_mem> <div class=card> <div class=card-header id=headingupload_mem> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#upload_mem aria-expanded aria-controls=upload_mem onclick="setAnchor('#upload_mem')"><span class=property-name>mem</span></button> </h2> </div> <div id=upload_mem class="collapse property-definition-div" aria-labelledby=headingupload_mem data-parent=#accordionupload_mem> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload onclick="anchorLink('upload')">upload</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload_mem onclick="anchorLink('upload_mem')">mem</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 256</span><br> </div> </div> </div> </div> <div class=accordion id=accordionupload_time> <div class=card> <div class=card-header id=headingupload_time> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#upload_time aria-expanded aria-controls=upload_time onclick="setAnchor('#upload_time')"><span class=property-name>time</span></button> </h2> </div> <div id=upload_time class="collapse property-definition-div" aria-labelledby=headingupload_time data-parent=#accordionupload_time> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload onclick="anchorLink('upload')">upload</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload_time onclick="anchorLink('upload_time')">time</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 60</span><br> </div> </div> </div> </div> <div class=accordion id=accordionupload_conda> <div class=card> <div class=card-header id=headingupload_conda> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#upload_conda aria-expanded aria-controls=upload_conda onclick="setAnchor('#upload_conda')"><span class=property-name>conda</span></button> </h2> </div> <div id=upload_conda class="collapse property-definition-div" aria-labelledby=headingupload_conda data-parent=#accordionupload_conda> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload onclick="anchorLink('upload')">upload</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload_conda onclick="anchorLink('upload_conda')">conda</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/envs/upload.yaml"</span><br> <span class=description><p>The default environment only provides hashing functions (<code>xxhash</code>, linux coreutils’ <code>sha</code><em>{nnn}</em><code>sum</code> collection, etc.) but depending on your needs you would want to provide a custom environment with additional tools (e.g. <code>sftp</code>, <code>rsync</code>, <code>curl</code>, <code>lftp</code>, custom specialized cloud uploaders, etc.)</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionupload_threads> <div class=card> <div class=card-header id=headingupload_threads> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#upload_threads aria-expanded aria-controls=upload_threads onclick="setAnchor('#upload_threads')"><span class=property-name>threads</span></button> </h2> </div> <div id=upload_threads class="collapse property-definition-div" aria-labelledby=headingupload_threads data-parent=#accordionupload_threads> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload onclick="anchorLink('upload')">upload</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload_threads onclick="anchorLink('upload_threads')">threads</a></div><span class="badge badge-dark value-type">Type: integer</span> <span class="badge badge-success default-value">Default: 1</span><br> </div> </div> </div> </div> <div class=accordion id=accordionupload_local> <div class=card> <div class=card-header id=headingupload_local> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#upload_local aria-expanded aria-controls=upload_local onclick="setAnchor('#upload_local')"><span class=property-name>local</span></button> </h2> </div> <div id=upload_local class="collapse property-definition-div" aria-labelledby=headingupload_local data-parent=#accordionupload_local> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload onclick="anchorLink('upload')">upload</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload_local onclick="anchorLink('upload_local')">local</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: true</span><br> <span class=description><p>Don’t dispatch the rule to the cluster for execution, run locally.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=upload_local_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">False</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionupload_consensus> <div class=card> <div class=card-header id=headingupload_consensus> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#upload_consensus aria-expanded aria-controls=upload_consensus onclick="setAnchor('#upload_consensus')"><span class=property-name>consensus</span></button> </h2> </div> <div id=upload_consensus class="collapse property-definition-div" aria-labelledby=headingupload_consensus data-parent=#accordionupload_consensus> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload onclick="anchorLink('upload')">upload</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload_consensus onclick="anchorLink('upload_consensus')">consensus</a></div><span class="badge badge-dark value-type">Type: enum (of string)</span> <span class="badge badge-success default-value">Default: "ambig"</span><br> <span class=description><p>When preparing data for upload, specifies which consensus sequence should be uploaded.</p> </span><div class=enum-value id=upload_consensus_enum> <h4>Must be one of:</h4> <ul class=list-group><li class="list-group-item enum-item">"ambig"</li><li class="list-group-item enum-item">"majority"</li></ul> </div> <br> <div class="badge badge-secondary">Example:</div> <br><div id=upload_consensus_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">majority</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionupload_checksum> <div class=card> <div class=card-header id=headingupload_checksum> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#upload_checksum aria-expanded aria-controls=upload_checksum onclick="setAnchor('#upload_checksum')"><span class=property-name>checksum</span></button> </h2> </div> <div id=upload_checksum class="collapse property-definition-div" aria-labelledby=headingupload_checksum data-parent=#accordionupload_checksum> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload onclick="anchorLink('upload')">upload</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload_checksum onclick="anchorLink('upload_checksum')">checksum</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>Generate checksum for each individual consensus sequence (if a consensus is regenerated, it will help determine whether the new file has changed content or is virtually the same as the previous).</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=upload_checksum_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionupload_orig_fastq> <div class=card> <div class=card-header id=headingupload_orig_fastq> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#upload_orig_fastq aria-expanded aria-controls=upload_orig_fastq onclick="setAnchor('#upload_orig_fastq')"><span class=property-name>orig_fastq</span></button> </h2> </div> <div id=upload_orig_fastq class="collapse property-definition-div" aria-labelledby=headingupload_orig_fastq data-parent=#accordionupload_orig_fastq> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload onclick="anchorLink('upload')">upload</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload_orig_fastq onclick="anchorLink('upload_orig_fastq')">orig_fastq</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>Also include the original <code>.fastq.gz</code> sequencing reads files from <code>raw_data/</code> in the list of files to be uploaded. See property <code>orig_cram</code> below for a compressed version and see output <code>dehumanized_raw_reads</code> and section <code>dehuman</code> for depleting reads from the host.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=upload_orig_fastq_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionupload_orig_cram> <div class=card> <div class=card-header id=headingupload_orig_cram> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#upload_orig_cram aria-expanded aria-controls=upload_orig_cram onclick="setAnchor('#upload_orig_cram')"><span class=property-name>orig_cram</span></button> </h2> </div> <div id=upload_orig_cram class="collapse property-definition-div" aria-labelledby=headingupload_orig_cram data-parent=#accordionupload_orig_cram> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload onclick="anchorLink('upload')">upload</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload_orig_cram onclick="anchorLink('upload_orig_cram')">orig_cram</a></div><span class="badge badge-dark value-type">Type: boolean</span> <span class="badge badge-success default-value">Default: false</span><br> <span class=description><p>Also include a compressed version of the original sequencing raw reads files from <code>raw_data/</code>. Similar to property <code>orig_fastq</code> above, but with reference-based compression.</p> </span> <br> <div class="badge badge-secondary">Example:</div> <br><div id=upload_orig_cram_ex1 class="jumbotron examples"><div class=highlight><pre><span></span><span class="l l-Scalar l-Scalar-Plain">True</span><span class=w></span>
</pre></div> </div> </div> </div> </div> </div> <div class=accordion id=accordionupload_script> <div class=card> <div class=card-header id=headingupload_script> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#upload_script aria-expanded aria-controls=upload_script onclick="setAnchor('#upload_script')"><span class=property-name>script</span></button> </h2> </div> <div id=upload_script class="collapse property-definition-div" aria-labelledby=headingupload_script data-parent=#accordionupload_script> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload onclick="anchorLink('upload')">upload</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload_script onclick="anchorLink('upload_script')">script</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: "{VPIPE_BASEDIR}/scripts/prepare_upload_symlinks.sh"</span><br> <span class=description><p>Custom script that assists and prepares uploads.</p> <p>It will receive the following positional parameters:</p> <ul> <li><em><OUTPUT></em>: the output file that must be created by the script.</li> <li><em><SAMPLE_ID></em>: a string (with no path separator slashes) that can be used as a name, uniquely identifying the sample and the date.</li> <li><em><SAMPLE_DIR></em>: the base directory of the sample.</li> <li><em><UPLOAD_FILES></em>…: a list of files to consider for upload</li> </ul> <p>For an example, see the default script <code>prepare_upload_symlinks.sh</code>, it generates symlinks that help tracking which samples are new and/or updated between runs of V-pipe and thus should be considered for upload.</p> </span> </div> </div> </div> </div> <div class=accordion id=accordionupload_options> <div class=card> <div class=card-header id=headingupload_options> <h2 class=mb-0> <button class="btn btn-link property-name-button" type=button data-toggle=collapse data-target=#upload_options aria-expanded aria-controls=upload_options onclick="setAnchor('#upload_options')"><span class=property-name>options</span></button> </h2> </div> <div id=upload_options class="collapse property-definition-div" aria-labelledby=headingupload_options data-parent=#accordionupload_options> <div class="card-body pl-5"> <div class=breadcrumbs>root <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload onclick="anchorLink('upload')">upload</a> <svg width=1em height=1em viewbox="0 0 16 16" class="bi bi-arrow-right-short" fill=currentColor xmlns=http://www.w3.org/2000/svg> <path fill-rule=evenodd d="M4 8a.5.5 0 0 1 .5-.5h5.793L8.146 5.354a.5.5 0 1 1 .708-.708l3 3a.5.5 0 0 1 0 .708l-3 3a.5.5 0 0 1-.708-.708L10.293 8.5H4.5A.5.5 0 0 1 4 8z"/> </svg> <a href=#upload_options onclick="anchorLink('upload_options')">options</a></div><span class="badge badge-dark value-type">Type: string</span> <span class="badge badge-success default-value">Default: ""</span><br> <span class=description><p>Named options to be passed to the script, before the positional parameters. E.g. for an extra configuration file with SFTP server information.</p> </span> </div> </div> </div> </div> </div> </div> </div> </div> <footer> <p class=generated-by-footer>Generated using <a href=https://github.com/coveooss/json-schema-for-humans>json-schema-for-humans</a> on 2024-07-05 at 19:32:38 +0200</p> </footer></body> </html>