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biobox/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
CI 71f1661df8 Build branch main with version main (219ba1d) 
Build pipeline: viash-hub.biobox.main-w9wb7

Source commit: 219ba1d3d0

Source message: Add more fq components (#179)

* add fq_lint, move fq_subsample, improve unit tests

* update changelog
2025-06-23 06:58:14 +00:00

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name: "bcftools_stats"
namespace: "bcftools"
version: "main"
authors:
- name: "Theodoro Gasperin Terra Camargo"
roles:
- "author"
info:
links:
email: "theodorogtc@gmail.com"
github: "tgaspe"
linkedin: "theodoro-gasperin-terra-camargo"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--input"
alternatives:
- "-i"
description: "Input VCF/BCF file. Maximum of two files."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
alternatives:
- "-o"
description: "Output txt statistics file."
info: null
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Options"
arguments:
- type: "string"
name: "--allele_frequency_bins"
alternatives:
- "--af_bins"
description: "Allele frequency bins, a list of bin values (0.1,0.5,1).\n"
info: null
example:
- "0.1,0.5,1"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--allele_frequency_bins_file"
alternatives:
- "--af_bins_file"
description: "Same as allele_frequency_bins, but in a file.\nFormat of file is\
\ one value per line. \ne.g. \n 0.1\n 0.5\n 1\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--allele_frequency_tag"
alternatives:
- "--af_tag"
description: "Allele frequency tag to use, by default estimated from AN,AC or\
\ GT.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--first_allele_only"
alternatives:
- "--first_only"
description: "Include only 1st allele at multiallelic sites.\n"
info: null
direction: "input"
- type: "string"
name: "--collapse"
alternatives:
- "--c"
description: "Treat as identical records with <snps|indels|both|all|some|none>.\n\
See https://samtools.github.io/bcftools/bcftools.html#common_options for details.\n"
info: null
required: false
choices:
- "snps"
- "indels"
- "both"
- "all"
- "some"
- "none"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--depth"
alternatives:
- "--d"
description: "Depth distribution: min,max,bin size.\n"
info: null
example:
- "0,500,1"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--exclude"
alternatives:
- "--e"
description: "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
\ for details.\n"
info: null
example:
- "QUAL < 30 && DP < 10"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--exons"
alternatives:
- "--E"
description: "tab-delimited file with exons for indel frameshifts statistics.\
\ \nThe columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions.\
\ \nThe file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2 -e3\
\ file.gz).\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--apply_filters"
alternatives:
- "--f"
description: "Require at least one of the listed FILTER strings (e.g. \"PASS,.\"\
).\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fasta_reference"
alternatives:
- "--F"
description: "Faidx indexed reference sequence file to determine INDEL context.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--include"
alternatives:
- "--i"
description: "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
\ for details.\n"
info: null
example:
- "QUAL >= 30 && DP >= 10"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--split_by_ID"
alternatives:
- "--I"
description: "Collect stats for sites with ID separately (known vs novel).\n"
info: null
direction: "input"
- type: "string"
name: "--regions"
alternatives:
- "--r"
description: "Restrict to comma-separated list of regions. \nFollowing formats\
\ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n"
info: null
example:
- "20:1000000-2000000"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--regions_file"
alternatives:
- "--R"
description: "Restrict to regions listed in a file. \nRegions can be specified\
\ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\
\ check manual.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--regions_overlap"
description: "This option controls how overlapping records are determined: \n\
set to 'pos' or '0' if the VCF record has to have POS inside a region (this\
\ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\
\ also overlapping records with POS outside a region should be included (this\
\ is the default behavior of -r/-R, \nand includes indels with POS at the end\
\ of a region, which are technically outside the region); \nor set to 'variant'\
\ or '2' to include only true overlapping variation (compare the full VCF representation\
\ \"TA>T-\" vs the true sequence variation \"A>-\").\n"
info: null
required: false
choices:
- "pos"
- "record"
- "variant"
- "0"
- "1"
- "2"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--samples"
alternatives:
- "--s"
description: "List of samples for sample stats, \"-\" to include all samples.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--samples_file"
alternatives:
- "--S"
description: "File of samples to include.\ne.g. \n sample1 1\n sample2 \
\ 2\n sample3 2\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--targets"
alternatives:
- "--t"
description: "Similar as -r, --regions, but the next position is accessed by streaming\
\ the whole VCF/BCF \nrather than using the tbi/csi index. Both -r and -t options\
\ can be applied simultaneously: -r uses the \nindex to jump to a region and\
\ -t discards positions which are not in the targets. Unlike -r, targets \n\
can be prefixed with \"^\" to request logical complement. For example, \"^X,Y,MT\"\
\ indicates that \nsequences X, Y and MT should be skipped. Yet another difference\
\ between the -t/-T and -r/-R is \nthat -r/-R checks for proper overlaps and\
\ considers both POS and the end position of an indel, \nwhile -t/-T considers\
\ the POS coordinate only (by default; see also --regions-overlap and --targets-overlap).\
\ \nNote that -t cannot be used in combination with -T.\nFollowing formats are\
\ supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n"
info: null
example:
- "20:1000000-2000000"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--targets_file"
alternatives:
- "--T"
description: "Similar to --regions_file option but streams rather than index-jumps.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--targets_overlaps"
description: "Include if POS in the region (0), record overlaps (1), variant overlaps\
\ (2).\n"
info: null
required: false
choices:
- "pos"
- "record"
- "variant"
- "0"
- "1"
- "2"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--user_tstv"
alternatives:
- "--u"
description: "Collect Ts/Tv stats for any tag using the given binning [0:1:100].\n\
Format is <TAG[:min:max:n]>.\nA subfield can be selected as e.g. 'PV4[0]', here\
\ the first value of the PV4 tag.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--verbose"
alternatives:
- "--v"
description: "Produce verbose per-site and per-sample output.\n"
info: null
direction: "input"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "Parses VCF or BCF and produces a txt stats file which can be plotted\
\ using plot-vcfstats.\nWhen two files are given, the program generates separate\
\ stats for intersection\nand the complements. By default only sites are compared,\
\ -s/-S must given to include\nalso sample columns.\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
keywords:
- "Stats"
- "VCF"
- "BCF"
license: "MIT/Expat, GNU"
references:
doi:
- "https://doi.org/10.1093/gigascience/giab008"
links:
repository: "https://github.com/samtools/bcftools"
homepage: "https://samtools.github.io/bcftools/"
documentation: "https://samtools.github.io/bcftools/bcftools.html#stats"
issue_tracker: "https://github.com/samtools/bcftools/issues"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "bcftools"
- "procps"
interactive: false
- type: "docker"
run:
- "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\
\ //p')\\\"\" > /var/software_versions.txt\n"
test_setup:
- type: "apt"
packages:
- "tabix"
interactive: false
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/bcftools/bcftools_stats/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/bcftools/bcftools_stats"
executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
viash_version: "0.9.4"
git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-37-g219ba1d"
package_config:
name: "biobox"
version: "main"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
authors:
- name: "Robrecht Cannoodt"
roles:
- "author"
- "maintainer"
info:
links:
email: "robrecht@data-intuitive.com"
github: "rcannood"
orcid: "0000-0003-3641-729X"
linkedin: "robrechtcannoodt"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Science Engineer"
- name: "Open Problems"
href: "https://openproblems.bio"
role: "Core Member"
- name: "Angela Oliveira Pisco"
roles:
- "author"
info:
role: "Contributor"
links:
github: "aopisco"
orcid: "0000-0003-0142-2355"
linkedin: "aopisco"
organizations:
- name: "Insitro"
href: "https://insitro.com"
role: "Director of Computational Biology"
- name: "Open Problems"
href: "https://openproblems.bio"
role: "Core Member"
- name: "Dorien Roosen"
roles:
- "author"
info:
links:
email: "dorien@data-intuitive.com"
github: "dorien-er"
linkedin: "dorien-roosen"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
- name: "Dries Schaumont"
roles:
- "author"
info:
links:
email: "dries@data-intuitive.com"
github: "DriesSchaumont"
orcid: "0000-0002-4389-0440"
linkedin: "dries-schaumont"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
- name: "Emma Rousseau"
roles:
- "author"
info:
links:
github: "emmarousseau"
linkedin: "emmarousseau1"
- name: "Jakub Majercik"
roles:
- "author"
info:
links:
email: "jakub@data-intuitive.com"
github: "jakubmajercik"
linkedin: "jakubmajercik"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Bioinformatics Engineer"
- name: "Kai Waldrant"
roles:
- "author"
info:
links:
github: "KaiWaldrant"
orcid: "0009-0003-8555-1361"
linkedin: "kaiwaldrant"
- name: "Leïla Paquay"
roles:
- "author"
info:
links:
github: "Leila011"
linkedin: "leilapaquay"
- name: "Sai Nirmayi Yasa"
roles:
- "author"
info:
links:
github: "sainirmayi"
linkedin: "sai-nirmayi-yasa"
- name: "Theodoro Gasperin Terra Camargo"
roles:
- "author"
info:
links:
email: "theodorogtc@gmail.com"
github: "tgaspe"
linkedin: "theodoro-gasperin-terra-camargo"
- name: "Toni Verbeiren"
roles:
- "author"
info:
links:
github: "tverbeiren"
linkedin: "verbeiren"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist and CEO"
- name: "Weiwei Schultz"
roles:
- "author"
info:
links:
linkedin: "weiwei-schultz"
organizations:
- name: "Janssen R&D US"
role: "Associate Director Data Sciences"
keywords:
- "bioinformatics"
- "modules"
- "sequencing"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/biobox"
issue_tracker: "https://github.com/viash-hub/biobox/issues"
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