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>
486 lines
14 KiB
YAML
486 lines
14 KiB
YAML
name: "bcftools_stats"
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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. Maximum of two files."
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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: true
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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 txt statistics 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: "string"
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name: "--allele_frequency_bins"
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alternatives:
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- "--af_bins"
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description: "Allele frequency bins, a list of bin values (0.1,0.5,1).\n"
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info: null
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example:
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- "0.1,0.5,1"
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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: "--allele_frequency_bins_file"
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alternatives:
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- "--af_bins_file"
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description: "Same as allele_frequency_bins, but in a file.\nFormat of file is\
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\ one value per line. \ne.g. \n 0.1\n 0.5\n 1\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: "--allele_frequency_tag"
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alternatives:
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- "--af_tag"
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description: "Allele frequency tag to use, by default estimated from AN,AC or\
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\ GT.\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: "--first_allele_only"
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alternatives:
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- "--first_only"
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description: "Include only 1st allele at multiallelic sites.\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--collapse"
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alternatives:
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- "--c"
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description: "Treat as identical records with <snps|indels|both|all|some|none>.\n\
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See https://samtools.github.io/bcftools/bcftools.html#common_options for details.\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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- "all"
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- "some"
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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: "string"
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name: "--depth"
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alternatives:
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- "--d"
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description: "Depth distribution: min,max,bin size.\n"
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info: null
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example:
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- "0,500,1"
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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: "--exclude"
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alternatives:
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- "--e"
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description: "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
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\ for details.\n"
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info: null
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example:
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- "QUAL < 30 && DP < 10"
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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: "--exons"
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alternatives:
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- "--E"
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description: "tab-delimited file with exons for indel frameshifts statistics.\
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\ \nThe columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions.\
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\ \nThe file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2 -e3\
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\ file.gz).\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: "--apply_filters"
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alternatives:
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- "--f"
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description: "Require at least one of the listed FILTER strings (e.g. \"PASS,.\"\
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).\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: "file"
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name: "--fasta_reference"
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alternatives:
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- "--F"
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description: "Faidx indexed reference sequence file to determine INDEL context.\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: "--include"
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alternatives:
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- "--i"
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description: "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
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\ for details.\n"
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info: null
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example:
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- "QUAL >= 30 && DP >= 10"
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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: "--split_by_ID"
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alternatives:
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- "--I"
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description: "Collect stats for sites with ID separately (known vs novel).\n"
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info: null
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direction: "input"
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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: "string"
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name: "--samples"
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alternatives:
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- "--s"
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description: "List of samples for sample stats, \"-\" to include all samples.\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: "file"
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name: "--samples_file"
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alternatives:
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- "--S"
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description: "File of samples to include.\ne.g. \n sample1 1\n sample2 \
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\ 2\n sample3 2\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: "--targets"
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alternatives:
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- "--t"
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description: "Similar as -r, --regions, but the next position is accessed by streaming\
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\ the whole VCF/BCF \nrather than using the tbi/csi index. Both -r and -t options\
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\ can be applied simultaneously: -r uses the \nindex to jump to a region and\
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\ -t discards positions which are not in the targets. Unlike -r, targets \n\
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can be prefixed with \"^\" to request logical complement. For example, \"^X,Y,MT\"\
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\ indicates that \nsequences X, Y and MT should be skipped. Yet another difference\
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\ between the -t/-T and -r/-R is \nthat -r/-R checks for proper overlaps and\
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\ considers both POS and the end position of an indel, \nwhile -t/-T considers\
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\ the POS coordinate only (by default; see also --regions-overlap and --targets-overlap).\
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\ \nNote that -t cannot be used in combination with -T.\nFollowing formats are\
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\ 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: "--targets_file"
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alternatives:
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- "--T"
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description: "Similar to --regions_file option but streams rather than index-jumps.\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: "--targets_overlaps"
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description: "Include if POS in the region (0), record overlaps (1), variant overlaps\
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\ (2).\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: "string"
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name: "--user_tstv"
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alternatives:
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- "--u"
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description: "Collect Ts/Tv stats for any tag using the given binning [0:1:100].\n\
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Format is <TAG[:min:max:n]>.\nA subfield can be selected as e.g. 'PV4[0]', here\
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\ the first value of the PV4 tag.\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: "--verbose"
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alternatives:
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- "--v"
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description: "Produce verbose per-site and per-sample output.\n"
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info: null
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direction: "input"
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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: "Parses VCF or BCF and produces a txt stats file which can be plotted\
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\ using plot-vcfstats.\nWhen two files are given, the program generates separate\
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\ stats for intersection\nand the complements. By default only sites are compared,\
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\ -s/-S must given to include\nalso sample columns.\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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- "Stats"
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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#stats"
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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"
|
|
mem4tib: "memory = 4398046511104.B"
|
|
mem8tib: "memory = 8796093022208.B"
|
|
mem16tib: "memory = 17592186044416.B"
|
|
mem32tib: "memory = 35184372088832.B"
|
|
mem64tib: "memory = 70368744177664.B"
|
|
mem128tib: "memory = 140737488355328.B"
|
|
mem256tib: "memory = 281474976710656.B"
|
|
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
|
|
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"
|
|
target_tag: "main"
|
|
namespace_separator: "/"
|
|
setup:
|
|
- type: "apt"
|
|
packages:
|
|
- "bcftools"
|
|
- "procps"
|
|
interactive: false
|
|
- type: "docker"
|
|
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
|
|
entrypoint: []
|
|
cmd: null
|
|
- type: "native"
|
|
id: "native"
|
|
build_info:
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|
config: "src/bcftools/bcftools_stats/config.vsh.yaml"
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|
runner: "executable"
|
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engine: "docker|native"
|
|
output: "target/executable/bcftools/bcftools_stats"
|
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executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
|
|
viash_version: "0.9.0"
|
|
git_commit: "7f8bcc2b3e1ffaac9778b6acb42420b19660d1a1"
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|
git_remote: "https://x-access-token:ghs_aSDBedV4vU66pddFDN6d8UEy0ZQApn08RAsh@github.com/viash-hub/biobox"
|
|
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"
|
|
issue_tracker: "https://github.com/viash-hub/biobox/issues"
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