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nextflow_schema.json
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nextflow_schema.json
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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/nextflow_schema.json",
"title": "genomic-medicine-sweden/nallo pipeline parameters",
"description": "Long-read variant calling pipeline",
"type": "object",
"$defs": {
"workflow_skip_options": {
"title": "Workflow skip options",
"type": "object",
"description": "Allows skipping certain parts of the pipeline",
"default": "",
"properties": {
"skip_qc": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip QC of reads",
"default": false
},
"skip_snv_calling": {
"type": "boolean",
"description": "Skip short variant calling",
"fa_icon": "fas fa-fast-forward",
"default": false
},
"skip_genome_assembly": {
"type": "boolean",
"description": "Skip genome assembly and assembly variant calling",
"fa_icon": "fas fa-fast-forward",
"default": false
},
"skip_alignment": {
"type": "boolean",
"description": "Skip read mapping (alignment)",
"fa_icon": "fas fa-fast-forward",
"default": false
},
"skip_methylation_pileups": {
"type": "boolean",
"description": "Skip generation of methylation pileups",
"fa_icon": "fas fa-fast-forward",
"default": false
},
"skip_repeat_calling": {
"type": "boolean",
"description": "Skip tandem repeat calling",
"fa_icon": "fas fa-fast-forward",
"default": false
},
"skip_repeat_annotation": {
"type": "boolean",
"description": "Skip tandem repeat annotation",
"fa_icon": "fas fa-fast-forward",
"default": false
},
"skip_phasing": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip phasing of variants and haplotagging of reads",
"default": false
},
"skip_snv_annotation": {
"type": "boolean",
"description": "Skip short variant annotation",
"default": false
},
"skip_sv_annotation": {
"type": "boolean",
"description": "Skip structural variant annotation",
"default": false
},
"skip_cnv_calling": {
"type": "boolean",
"description": "Skip CNV calling",
"default": false
},
"skip_call_paralogs": {
"type": "boolean",
"description": "Skip the calling of specific paralogous genes",
"default": false
},
"skip_rank_variants": {
"type": "boolean",
"description": "Skip ranking of short variants",
"default": false
}
},
"fa_icon": "fas fa-american-sign-language-interpreting"
},
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"schema": "assets/schema_input.json",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"multiqc_title": {
"type": "string",
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature"
},
"cadd_prescored_indels": {
"type": "string",
"exists": true,
"format": "directory-path",
"fa_icon": "fas fa-file",
"description": "Path to a directory containing prescored indels for CADD.",
"help_text": "This folder contains the compressed files and indexes that would otherwise be in data/prescored folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation."
},
"cadd_resources": {
"type": "string",
"exists": true,
"format": "directory-path",
"fa_icon": "fas fa-file",
"description": "Path to a directory containing CADD annotations.",
"help_text": "This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation."
},
"par_regions": {
"type": "string",
"description": "Provide a bed file of chrX and chrY PAR regions for dipcall and DeepVariant",
"format": "file-path",
"exists": true
},
"tandem_repeats": {
"type": "string",
"format": "file-path",
"description": "A tandem repeat BED file for sniffles",
"pattern": "^\\S+\\.bed$",
"exists": true
},
"trgt_repeats": {
"type": "string",
"description": "A BED file with repeats to be genotyped with TRGT",
"format": "file-path",
"exists": true
},
"echtvar_snv_databases": {
"type": "string",
"pattern": "^\\S+\\.csv$",
"format": "file-path",
"mimetype": "text/csv",
"schema": "/assets/schema_snp_db.json",
"description": "A csv file with echtvar databases to annotate SNVs with",
"exists": true
},
"svdb_sv_databases": {
"type": "string",
"exists": true,
"format": "file-path",
"description": "Databases used for structural variant annotation in vcf format.",
"fa_icon": "fas fa-file-csv",
"help_text": "Path to comma-separated file containing information about the databases used for structural variant annotation.",
"pattern": "^\\S+\\.csv$",
"mimetype": "text/csv",
"schema": "assets/svdb_query_vcf_schema.json"
},
"stranger_repeat_catalog": {
"type": "string",
"description": "A variant catalog json-file for stranger",
"format": "file-path",
"exists": true
},
"variant_consequences_snvs": {
"type": "string",
"description": "File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SNVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html",
"fa_icon": "fas fa-file-csv"
},
"variant_consequences_svs": {
"type": "string",
"description": "File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html",
"fa_icon": "fas fa-file-csv"
},
"vep_cache": {
"type": "string",
"description": "A path to the VEP cache location",
"format": "path",
"exists": true
},
"target_regions": {
"type": "string",
"pattern": "^\\S+\\.bed$",
"format": "file-path",
"description": "A BED file with regions of interest, used to limit variant calling.",
"exists": true
},
"hificnv_expected_xy_cn": {
"type": "string",
"format": "file-path",
"description": "A BED file containing expected copy number regions for XY samples.",
"exists": true
},
"hificnv_expected_xx_cn": {
"type": "string",
"format": "file-path",
"description": "A BED file containing expected copy number regions for XX samples.",
"exists": true
},
"hificnv_excluded_regions": {
"type": "string",
"format": "file-path",
"description": "A BED file specifying regions to exclude with HiFiCNV, such as centromeres.",
"exists": true
},
"genmod_reduced_penetrance": {
"type": "string",
"exists": true,
"format": "path",
"fa_icon": "fas fa-file-csv",
"description": "A file with gene ids that have reduced penetrance. For use with genmod."
},
"genmod_score_config_snvs": {
"type": "string",
"exists": true,
"format": "path",
"fa_icon": "fas fa-file",
"description": "A SNV rank model config file for genmod."
},
"genmod_score_config_svs": {
"type": "string",
"exists": true,
"format": "path",
"fa_icon": "fas fa-file",
"description": "A SV rank model config file for genmod."
},
"somalier_sites": {
"type": "string",
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"description": "A VCF of known polymorphic sites for somalier",
"format": "file-path",
"exists": true
},
"pipelines_testdata_base_path": {
"type": "string",
"fa_icon": "far fa-check-circle",
"description": "Base URL or local path to location of pipeline test dataset files",
"default": "https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/ba720cd29322036d966ab3e4bc4c3d03e1731af5/",
"hidden": true
}
}
},
"reference_genome_options": {
"title": "Reference genome options",
"type": "object",
"fa_icon": "fas fa-dna",
"description": "Reference genome related files and options required for the workflow.",
"properties": {
"fasta": {
"type": "string",
"description": "Reference genome",
"pattern": "^.*\\.(fasta|fa|fna)(\\.gz)?$",
"format": "file-path",
"exists": true
}
}
},
"institutional_config_options": {
"title": "Institutional config options",
"type": "object",
"fa_icon": "fas fa-university",
"description": "Parameters used to describe centralised config profiles. These should not be edited.",
"help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"properties": {
"custom_config_version": {
"type": "string",
"description": "Git commit id for Institutional configs.",
"default": "master",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"custom_config_base": {
"type": "string",
"description": "Base directory for Institutional configs.",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"hidden": true,
"help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
"fa_icon": "fas fa-users-cog"
},
"config_profile_name": {
"type": "string",
"description": "Institutional config name.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_description": {
"type": "string",
"description": "Institutional config description.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_contact": {
"type": "string",
"description": "Institutional config contact information.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_url": {
"type": "string",
"description": "Institutional config URL link.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
}
}
},
"generic_options": {
"title": "Generic options",
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
},
"email_on_fail": {
"type": "string",
"description": "Email address for completion summary, only when pipeline fails.",
"fa_icon": "fas fa-exclamation-triangle",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
"help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
"hidden": true
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true
},
"max_multiqc_email_size": {
"type": "string",
"description": "File size limit when attaching MultiQC reports to summary emails.",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"default": "25.MB",
"fa_icon": "fas fa-file-upload",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"hook_url": {
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-people-group",
"help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
"hidden": true
},
"multiqc_config": {
"type": "string",
"format": "file-path",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"multiqc_logo": {
"type": "string",
"description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
"fa_icon": "fas fa-image",
"hidden": true
},
"multiqc_methods_description": {
"type": "string",
"description": "Custom MultiQC yaml file containing HTML including a methods description.",
"fa_icon": "fas fa-cog"
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
}
}
},
"workflow_options": {
"title": "Workflow options",
"type": "object",
"description": "Workflow options specific to genomic-medicine-sweden/nallo",
"default": "",
"properties": {
"preset": {
"type": "string",
"default": "revio",
"description": "Enable or disable certain parts of the pipeline by default, depending on data type (`revio`, `pacbio`, `ONT_R10`)",
"enum": ["revio", "pacbio", "ONT_R10"]
},
"snv_caller": {
"type": "string",
"default": "deepvariant",
"description": "Which short variant software to use (`deepvariant`)",
"enum": ["deepvariant"]
},
"sv_caller": {
"type": "string",
"default": "severus",
"description": "Which structural variant caller to use (`severus`, `sniffles`)",
"enum": ["severus", "sniffles"]
},
"phaser": {
"type": "string",
"default": "longphase",
"description": "Which phasing software to use (`longphase`, `whatshap`, `hiphase`)",
"enum": ["longphase", "whatshap", "hiphase"]
},
"hifiasm_mode": {
"type": "string",
"description": "Run hifiasm in hifi-only or hifi-trio mode (`hifi-only`, `trio-binning`)",
"enum": ["hifi-only", "trio-binning"],
"default": "hifi-only"
},
"alignment_processes": {
"type": "integer",
"minimum": 1,
"default": 8,
"description": "If alignment_processes is bigger than 1, input files will be split and aligned in parallel to reduce processing time."
},
"snv_calling_processes": {
"type": "integer",
"default": 13,
"description": "If snv_calling_processes is bigger than 1, short variant calling will be done in parallel to reduce processing time.",
"minimum": 1
},
"vep_cache_version": {
"type": "integer",
"default": 110,
"description": "VEP cache version"
},
"vep_plugin_files": {
"type": "string",
"mimetype": "text/csv",
"description": "A csv file with vep_files as header, and then paths to vep plugin files. Paths to pLI_values.txt and LoFtool_scores.txt are required.",
"schema": "assets/vep_plugin_files_schema.json"
},
"filter_variants_hgnc_ids": {
"type": "string",
"pattern": "^\\S+\\.(csv|tsv)$",
"description": "A tsv/csv file with a `hgnc_ids` column header, and then one numerical HGNC ID per row. E.g. `4281` or `HGNC:4281`.",
"format": "file-path",
"exits": true,
"schema": "assets/schema_hgnc_ids.json"
},
"filter_snvs_expression": {
"type": "string",
"default": "",
"description": "An expression that is passed to bcftools view to filter SNVs, e.g. --filter_snvs_expression \"-e 'INFO/AQ>60'\""
},
"filter_svs_expression": {
"type": "string",
"default": "",
"description": "An expression that is passed to bcftools view to filter SVs, e.g. --filter_svs_expression \"-e 'INFO/AQ>60'\""
},
"deepvariant_model_type": {
"type": "string",
"default": "PACBIO",
"description": "Sets the model type used for DeepVariant. This is set automatically using `--preset` by default.",
"hidden": true,
"enum": ["PACBIO", "ONT_R104"]
},
"minimap2_read_mapping_preset": {
"type": "string",
"description": "Sets the minimap2-preset (-x) for read alignment. This is set automatically using the pipeline `--preset` by default.",
"hidden": true,
"enum": ["map-hifi", "map-ont", "lr:hq", "lr:hqae"],
"default": "map-hifi"
},
"extra_modkit_options": {
"type": "string",
"hidden": true,
"description": "Extra options to modkit, used for test profile."
},
"extra_vep_options": {
"type": "string",
"hidden": true,
"description": "Extra options to VEP, used for test profile."
},
"extra_paraphase_options": {
"type": "string",
"hidden": true,
"description": "Extra options to Paraphase, used for test profile."
},
"extra_hifiasm_options": {
"type": "string",
"hidden": true,
"description": "Extra options to hifiasm, used for test profile."
}
},
"required": ["preset"]
}
},
"allOf": [
{
"$ref": "#/$defs/workflow_skip_options"
},
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/reference_genome_options"
},
{
"$ref": "#/$defs/institutional_config_options"
},
{
"$ref": "#/$defs/generic_options"
},
{
"$ref": "#/$defs/workflow_options"
},
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/reference_genome_options"
},
{
"$ref": "#/$defs/institutional_config_options"
},
{
"$ref": "#/$defs/generic_options"
}
]
}