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"
    description: "Input VCF/BCF file(s). Maximum of two files can be provided.\nWhen\
      \ two files are given, the program generates separate stats \nfor intersection\
      \ and the complements.\n"
    info: null
    example:
    - "input.vcf.gz"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    alternatives:
    - "-o"
    description: "Write output to a file. The output is a text file which can be \n\
      plotted using plot-vcfstats.\n"
    info: null
    example:
    - "stats.txt"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "string"
    name: "--af_bins"
    description: "Allele frequency bins, a list of comma-separated bin values.\n"
    info: null
    example:
    - "0.1,0.5,1"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--af_tag"
    description: "Allele frequency tag to use, by default estimated from AN,AC or\
      \ GT.\n"
    info: null
    example:
    - "AF"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--collapse"
    alternatives:
    - "-c"
    description: "Treat as identical records with <snps|indels|both|all|some|none>.\n"
    info: null
    example:
    - "snps"
    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 [0:200:1].\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.\n"
    info: null
    example:
    - "QUAL < 30"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--exons"
    alternatives:
    - "-E"
    description: "Tab-delimited file with exons for indel frameshifts statistics.\n\
      The columns of the file are CHR, FROM, TO, with 1-based positions.\nThe file\
      \ should be BGZF-compressed and indexed with tabix.\n"
    info: null
    example:
    - "exons.bed.gz"
    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.\n"
    info: null
    example:
    - "PASS,."
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fasta_ref"
    alternatives:
    - "-F"
    description: "Faidx indexed reference sequence file to determine INDEL context.\n"
    info: null
    example:
    - "reference.fa"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--first_allele_only"
    alternatives:
    - "--1st-allele-only"
    description: "Include only 1st allele at multiallelic sites.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--include"
    alternatives:
    - "-i"
    description: "Select sites for which the expression is true.\n"
    info: null
    example:
    - "QUAL >= 30"
    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.\n"
    info: null
    example:
    - "chr20:1000000-2000000"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--regions_file"
    alternatives:
    - "-R"
    description: "Restrict to regions listed in a file.\n"
    info: null
    example:
    - "regions.bed"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--regions_overlap"
    description: "Include if POS in the region (pos), record overlaps (record), \n\
      variant overlaps (variant). Can also use numeric equivalents 0, 1, 2.\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
    example:
    - "sample1,sample2"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--samples_file"
    alternatives:
    - "-S"
    description: "File of samples to include.\n"
    info: null
    example:
    - "samples.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--targets"
    alternatives:
    - "-t"
    description: "Similar to regions, but streams rather than using index.\nTargets\
      \ can be prefixed with \"^\" for logical complement.\n"
    info: null
    example:
    - "chr20:1000000-2000000"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--targets_file"
    alternatives:
    - "-T"
    description: "Similar to regions_file but streams rather than index-jumps.\n"
    info: null
    example:
    - "targets.bed"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--targets_overlap"
    description: "Include if POS in the region (pos), record overlaps (record), \n\
      variant overlaps (variant). Can also use numeric equivalents 0, 1, 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.\nFormat\
      \ is TAG[:min:max:n]. Default binning is [0:1:100].\n"
    info: null
    example:
    - "QUAL:0:40:40"
    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:
  - "bcftools"
  - "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: "quay.io/biocontainers/bcftools:1.22--h3a4d415_1"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "bcftools --version | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n"
  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: "9991e9a4f5ddd5085a4e2becf962950b1daf594b"
  git_remote: "https://github.com/viash-hub/biobox"
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'"
  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"
