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Ampliseq Version 2.3.0
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@d4straub d4straub released this 04 Apr 11:37
· 1324 commits to master since this release
2.3.0
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nf-core/ampliseq version 2.3.0 - 2022-04-04

Summary of changes

  • Added Barrnap that annotates whether ASV sequences are SSUs and filter on demand
  • Primer sequences are now not required any more and cutadapt can be skipped
  • Updated to nf-core template 2.3.2
  • Fixed some bugs

Detailed changes

Added

  • #385 - --skip_cutadapt allows to skip primer trimmimg.
  • #390, #408 - Add values to option --cut_its, specifying which ITS part to use. Also, add option --its_partial <x> to allow partial ITS sequences longer than given cutoff.
  • #395 - --seed specifies the random seed.
  • #396 - Barrnap annotates ASV sequences for SSU's, it can be skipped with --skip_barrnap. --filter_ssu takes a comma separated list of "bac,arc,mito,euk" and enables SSU filtering depending on Barrnap (default: off).
  • #397 - Complement README.md with links to the nf-core bytesize 25 (nf-core/ampliseq).

Changed

  • #385 - --FW_primer and --RV_primer are not obligatory any more, however primer sequences are still required with cutadapt (i.e. without --skip_cutadapt), --qiime_ref_taxonomy, and --cut_dada_ref_taxonomy (cuts reference with primer sequences).

Fixed

  • #384 - For QIIME2 beta diversity, make directory before execution.
  • #394 - Prevent simultaneous usage of --qiime_ref_taxonomy and --classifier.
  • #402, #410 - Template update for nf-core/tools version 2.3.2
  • #403 - Limit number of files for DADA2_QUALITY (plotQualityProfile) by read numbers.
  • #405 - Fix omitting taxonomic filtering (QIIME2_FILTERTAXA).
  • #404 - Rephrase error message for empty input files and empty files after trimming with cutadapt.
  • #407 - Fix reformatting script for Unite.

Dependencies

Tool Previous version New version
MultiQC 1.11 1.12
Assets 2
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