CI
6f2f840fd9
Build pipeline: viash-hub.biobox.main-zp6tq
Source commit: 7f8bcc2b3e
Source message: BD rhapsody sequence analysis (#96)
* wip
* fix test
* add help
* update 2.2 args
* fix bug
* extend test data
* output separate files
* analyse missing args
* tweaks to test
* fix script
* fix test
* fix test
* move small reference
* wip generate wta test data
* don't forget about umi in r1
* remove unneeded pkg
* load reference in memory just once
* fix random choices
* extend test
* add abc immunediscoverypanel
* wip abc testing code
* fix abc test; need unique instrument, run and flowcell ids for each sample
* add smk data
* add entry to changelog
* remove old test file
* adapt test for missing read
* update description
* add comment
* ensure cwl files are absolute
* Apply suggestions from code review
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
* fix suggestion
* newer pipelines have docker requirements as a hint instead of a strict requirement
* rename str to content
* remove deleted resources
* fix containers
* fix script
* fix suggestion
* fix suggestion...
* fix test
* fix component name
* fix test
* apply suggestions
* fix test
* added note
* fix changelog
* fix changelog again
* splitting hairs here
---------
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
444 lines
12 KiB
YAML
444 lines
12 KiB
YAML
name: "bcftools_norm"
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namespace: "bcftools"
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version: "main"
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authors:
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- name: "Theodoro Gasperin Terra Camargo"
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roles:
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- "author"
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info:
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links:
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email: "theodorogtc@gmail.com"
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github: "tgaspe"
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linkedin: "theodoro-gasperin-terra-camargo"
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organizations:
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- name: "Data Intuitive"
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href: "https://www.data-intuitive.com"
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role: "Bioinformatician"
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argument_groups:
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- name: "Inputs"
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arguments:
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- type: "file"
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name: "--input"
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alternatives:
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- "-i"
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description: "Input VCF/BCF file."
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info: null
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Outputs"
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arguments:
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- type: "file"
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name: "--output"
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alternatives:
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- "-o"
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description: "Output normalized VCF/BCF file."
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info: null
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must_exist: true
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create_parent: true
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required: true
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- name: "Options"
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arguments:
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- type: "boolean_true"
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name: "--atomize"
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alternatives:
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- "-a"
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description: "Decompose complex variants (e.g., MNVs become consecutive SNVs).\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--atom_overlaps"
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description: "Use the star allele (*) for overlapping alleles or set to missing\
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\ (.).\n"
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info: null
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required: false
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choices:
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- "."
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- "*"
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--check_ref"
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alternatives:
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- "-c"
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description: "Check REF alleles and exit (e), warn (w), exclude (x), or set (s)\
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\ bad sites.\n"
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info: null
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required: false
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choices:
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- "e"
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- "w"
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- "x"
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- "s"
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--remove_duplicates"
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alternatives:
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- "-d"
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description: "Remove duplicate snps, indels, both, all, exact matches, or none\
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\ (old -D option)."
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info: null
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required: false
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choices:
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- "snps"
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- "indels"
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- "both"
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- "all"
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- "exact"
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- "none"
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--fasta_ref"
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alternatives:
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- "-f"
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description: "Reference fasta sequence file."
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info: null
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must_exist: true
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create_parent: true
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--force"
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description: "Try to proceed even if malformed tags are encountered. \nExperimental,\
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\ use at your own risk.\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--keep_sum"
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description: "Keep vector sum constant when splitting multiallelics (see github\
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\ issue #360).\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--multiallelics"
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alternatives:
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- "-m"
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description: "Split multiallelics (-) or join biallelics (+), type: snps, indels,\
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\ both, any [default: both].\n"
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info: null
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required: false
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choices:
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- "+snps"
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- "+indels"
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- "+both"
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- "+any"
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- "-snps"
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- "-indels"
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- "-both"
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- "-any"
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--no_version"
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description: "Do not append version and command line information to the header."
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--do_not_normalize"
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alternatives:
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- "-N"
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description: "Do not normalize indels (with -m or -c s)."
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info: null
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direction: "input"
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- type: "string"
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name: "--output_type"
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alternatives:
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- "--O"
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description: "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed\
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\ BCF\n v: uncompressed VCF\n"
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info: null
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required: false
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choices:
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- "u"
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- "z"
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- "b"
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- "v"
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--old_rec_tag"
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description: "Annotate modified records with INFO/STR indicating the original\
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\ variant."
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--regions"
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alternatives:
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- "--r"
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description: "Restrict to comma-separated list of regions. \nFollowing formats\
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\ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…].\n"
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info: null
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example:
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- "20:1000000-2000000"
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--regions_file"
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alternatives:
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- "--R"
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description: "Restrict to regions listed in a file. \nRegions can be specified\
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\ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\
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\ check manual.\n"
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info: null
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must_exist: true
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create_parent: true
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--regions_overlap"
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description: "This option controls how overlapping records are determined: \n\
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set to 'pos' or '0' if the VCF record has to have POS inside a region (this\
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\ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\
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\ also overlapping records with POS outside a region should be included (this\
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\ is the default behavior of -r/-R, \nand includes indels with POS at the end\
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\ of a region, which are technically outside the region); \nor set to 'variant'\
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\ or '2' to include only true overlapping variation (compare the full VCF representation\
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\ \"TA>T-\" vs the true sequence variation \"A>-\").\n"
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info: null
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required: false
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choices:
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- "pos"
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- "record"
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- "variant"
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- "0"
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- "1"
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- "2"
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "integer"
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name: "--site_win"
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alternatives:
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- "-w"
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description: "Buffer for sorting lines that changed position during realignment.\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--strict_filter"
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alternatives:
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- "-s"
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description: "When merging (-m+), merged site is PASS only if all sites being\
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\ merged PASS."
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info: null
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direction: "input"
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- type: "string"
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name: "--targets"
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alternatives:
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- "-t"
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description: "Similar to --regions but streams rather than index-jumps."
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info: null
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example:
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- "20:1000000-2000000"
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--targets_file"
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alternatives:
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- "-T"
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description: "Similar to --regions_file but streams rather than index-jumps."
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info: null
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must_exist: true
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create_parent: true
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--targets_overlap"
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description: "Include if POS in the region (0), record overlaps (1), variant overlaps\
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\ (2).\nSimilar to --regions_overlap.\n"
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info: null
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required: false
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choices:
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- "pos"
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- "record"
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- "variant"
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- "0"
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- "1"
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- "2"
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direction: "input"
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multiple: false
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multiple_sep: ";"
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resources:
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- type: "bash_script"
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path: "script.sh"
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is_executable: true
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description: "Left-align and normalize indels, check if REF alleles match the reference,\
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\ split multiallelic sites into multiple rows; \nrecover multiallelics from multiple\
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\ rows. \n"
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test_resources:
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- type: "bash_script"
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path: "test.sh"
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is_executable: true
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info: null
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status: "enabled"
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requirements:
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commands:
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- "ps"
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keywords:
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- "Normalize"
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- "VCF"
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- "BCF"
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license: "MIT/Expat, GNU"
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references:
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doi:
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- "https://doi.org/10.1093/gigascience/giab008"
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links:
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repository: "https://github.com/samtools/bcftools"
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homepage: "https://samtools.github.io/bcftools/"
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documentation: "https://samtools.github.io/bcftools/bcftools.html#norm"
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issue_tracker: "https://github.com/samtools/bcftools/issues"
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runners:
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- type: "executable"
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id: "executable"
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docker_setup_strategy: "ifneedbepullelsecachedbuild"
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- type: "nextflow"
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id: "nextflow"
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directives:
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tag: "$id"
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auto:
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simplifyInput: true
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simplifyOutput: false
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transcript: false
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publish: false
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config:
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labels:
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mem1gb: "memory = 1000000000.B"
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mem2gb: "memory = 2000000000.B"
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mem5gb: "memory = 5000000000.B"
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mem10gb: "memory = 10000000000.B"
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mem20gb: "memory = 20000000000.B"
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mem50gb: "memory = 50000000000.B"
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mem100gb: "memory = 100000000000.B"
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mem200gb: "memory = 200000000000.B"
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mem500gb: "memory = 500000000000.B"
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mem1tb: "memory = 1000000000000.B"
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mem2tb: "memory = 2000000000000.B"
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mem5tb: "memory = 5000000000000.B"
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mem10tb: "memory = 10000000000000.B"
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mem20tb: "memory = 20000000000000.B"
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mem50tb: "memory = 50000000000000.B"
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mem100tb: "memory = 100000000000000.B"
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mem200tb: "memory = 200000000000000.B"
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mem500tb: "memory = 500000000000000.B"
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mem1gib: "memory = 1073741824.B"
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mem2gib: "memory = 2147483648.B"
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mem4gib: "memory = 4294967296.B"
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mem8gib: "memory = 8589934592.B"
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mem16gib: "memory = 17179869184.B"
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mem32gib: "memory = 34359738368.B"
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mem64gib: "memory = 68719476736.B"
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mem128gib: "memory = 137438953472.B"
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mem256gib: "memory = 274877906944.B"
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mem512gib: "memory = 549755813888.B"
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mem1tib: "memory = 1099511627776.B"
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mem2tib: "memory = 2199023255552.B"
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mem4tib: "memory = 4398046511104.B"
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mem8tib: "memory = 8796093022208.B"
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mem16tib: "memory = 17592186044416.B"
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mem32tib: "memory = 35184372088832.B"
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mem64tib: "memory = 70368744177664.B"
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mem128tib: "memory = 140737488355328.B"
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mem256tib: "memory = 281474976710656.B"
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mem512tib: "memory = 562949953421312.B"
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cpu1: "cpus = 1"
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cpu2: "cpus = 2"
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cpu5: "cpus = 5"
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cpu10: "cpus = 10"
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cpu20: "cpus = 20"
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cpu50: "cpus = 50"
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cpu100: "cpus = 100"
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cpu200: "cpus = 200"
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cpu500: "cpus = 500"
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cpu1000: "cpus = 1000"
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debug: false
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container: "docker"
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engines:
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- type: "docker"
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id: "docker"
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image: "debian:stable-slim"
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target_registry: "images.viash-hub.com"
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target_tag: "main"
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namespace_separator: "/"
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setup:
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- type: "apt"
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packages:
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- "bcftools"
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- "procps"
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interactive: false
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- type: "docker"
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run:
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- "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\
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\ //p')\\\"\" > /var/software_versions.txt\n"
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test_setup:
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- type: "apt"
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packages:
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- "tabix"
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interactive: false
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entrypoint: []
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cmd: null
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- type: "native"
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id: "native"
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build_info:
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config: "src/bcftools/bcftools_norm/config.vsh.yaml"
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runner: "executable"
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engine: "docker|native"
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output: "target/executable/bcftools/bcftools_norm"
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executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
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viash_version: "0.9.0"
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git_commit: "7f8bcc2b3e1ffaac9778b6acb42420b19660d1a1"
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git_remote: "https://x-access-token:ghs_aSDBedV4vU66pddFDN6d8UEy0ZQApn08RAsh@github.com/viash-hub/biobox"
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git_tag: "v0.2.0-3-g7f8bcc2"
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package_config:
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name: "biobox"
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version: "main"
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description: "A collection of bioinformatics tools for working with sequence data.\n"
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info: null
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viash_version: "0.9.0"
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source: "src"
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target: "target"
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config_mods:
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- ".requirements.commands := ['ps']\n"
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- ".engines += { type: \"native\" }"
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- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
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- ".engines[.type == 'docker'].target_tag := 'main'"
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keywords:
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- "bioinformatics"
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- "modules"
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- "sequencing"
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license: "MIT"
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organization: "vsh"
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links:
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repository: "https://github.com/viash-hub/biobox"
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issue_tracker: "https://github.com/viash-hub/biobox/issues"
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