name: "bcftools_stats"
namespace: "bcftools"
version: "add_sgdemux"
authors:
- name: "Theodoro Gasperin Terra Camargo"
  roles:
  - "author"
  info:
    links:
      email: "theodorogtc@gmail.com"
      github: "tgaspe"
      linkedin: "theodoro-gasperin-terra-camargo"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Bioinformatician"
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"
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: "add_sgdemux"
  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: "0.9.0"
  git_commit: "402ad6a813c0d0b141bbf8f9a3aab9c270a74812"
  git_remote: "https://x-access-token:ghs_VWGBwCOTHxXRJ07uVE94xFn8UJ2FmS0FLhmc@github.com/viash-hub/biobox"
  git_tag: "v0.2.0-27-g402ad6a"
package_config:
  name: "biobox"
  version: "add_sgdemux"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
  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 := 'add_sgdemux'"
  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"
