name: "bcftools_annotate"
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."
    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 annotated file."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  description: "For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html.\n\
    For more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate.\n"
  arguments:
  - type: "file"
    name: "--annotations"
    alternatives:
    - "--a"
    description: "VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+\
      \ . \n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--columns"
    alternatives:
    - "--c"
    description: "List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG.\
      \ \nSee man page for details.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--columns_file"
    alternatives:
    - "--C"
    description: "Read -c columns from FILE, one name per row, with optional --merge_logic\
      \ TYPE: NAME[ TYPE].\n"
    info: null
    must_exist: true
    create_parent: true
    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: "boolean_true"
    name: "--force"
    description: "continue even when parsing errors, such as undefined tags, are encountered.\
      \ \nNote this can be an unsafe operation and can result in corrupted BCF files.\
      \ \nIf this option is used, make sure to sanity check the result thoroughly.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--header_line"
    alternatives:
    - "--H"
    description: "Header line which should be appended to the VCF header, can be given\
      \ multiple times.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--header_lines"
    alternatives:
    - "--h"
    description: "File with header lines to append to the VCF header.\nFor example:\n\
      \  ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description=\"Example header\
      \ line\">\n  ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description=\"Yet another\
      \ header line\">\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--set_id"
    alternatives:
    - "--I"
    description: "Set ID column using a `bcftools query`-like expression, see man\
      \ page for details.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--include"
    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: "--keep_sites"
    alternatives:
    - "--k"
    description: "Leave --include/--exclude sites unchanged instead of discarding\
      \ them.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--merge_logic"
    alternatives:
    - "--l"
    description: "When multiple regions overlap a single record, this option defines\
      \ how to treat multiple annotation values.\nSee man page for more details.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--mark_sites"
    alternatives:
    - "--m"
    description: "Annotate sites which are present (\"+\") or absent (\"-\") in the\
      \ -a file with a new INFO/TAG flag.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--min_overlap"
    description: "Minimum overlap required as a fraction of the variant in the annotation\
      \ -a file (ANN), \nin the target VCF file (:VCF), or both for reciprocal overlap\
      \ (ANN:VCF). \nBy default overlaps of arbitrary length are sufficient. \nThe\
      \ option can be used only with the tab-delimited annotation -a file and with\
      \ BEG and END columns present.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--no_version"
    description: "Do not append version and command line information to the output\
      \ VCF header.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--output_type"
    alternatives:
    - "--O"
    description: "Output type:\n  u: uncompressed BCF\n  z: compressed VCF\n  b: compressed\
      \ BCF\n  v: uncompressed VCF\n"
    info: null
    required: false
    choices:
    - "u"
    - "z"
    - "b"
    - "v"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--pair_logic"
    description: "Controls how to match records from the annotation file to the target\
      \ VCF. \nEffective only when -a is a VCF or BCF file. \nThe option replaces\
      \ the former uninuitive --collapse. \nSee Common Options for more.\n"
    info: null
    required: false
    choices:
    - "snps"
    - "indels"
    - "both"
    - "all"
    - "some"
    - "exact"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - 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: "file"
    name: "--rename_annotations"
    description: "Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--rename_chromosomes"
    description: "Rename chromosomes according to the map in file, with \"old_name\
      \ new_name\\n\" pairs \nseparated by whitespaces, each on a separate line.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--samples"
    description: "Subset of samples to annotate.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--samples_file"
    description: "Subset of samples to annotate in file format.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--single_overlaps"
    description: "Use this option to keep memory requirements low with very large\
      \ annotation files. \nNote, however, that this comes at a cost, only single\
      \ overlapping intervals are considered in this mode. \nThis was the default\
      \ mode until the commit af6f0c9 (Feb 24 2019).\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--remove"
    alternatives:
    - "--x"
    description: "List of annotations to remove. \nUse \"FILTER\" to remove all filters\
      \ or \"FILTER/SomeFilter\" to remove a specific filter. \nSimilarly, \"INFO\"\
      \ can be used to remove all INFO tags and \"FORMAT\" to remove all FORMAT tags\
      \ except GT. \nTo remove all INFO tags except \"FOO\" and \"BAR\", use \"^INFO/FOO,INFO/BAR\"\
      \ (and similarly for FORMAT and FILTER). \n\"INFO\" can be abbreviated to \"\
      INF\" and \"FORMAT\" to \"FMT\".\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--verbosity"
    alternatives:
    - "-v"
    description: "Verbosity level.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Add or remove annotations from a VCF/BCF file.\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "test_helpers.sh"
info: null
status: "enabled"
scope:
  image: "public"
  target: "public"
requirements:
  commands:
  - "bcftools"
  - "ps"
keywords:
- "Annotate"
- "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#annotate"
  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:
    - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\
      \ //p')\\\"\" > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/bcftools/bcftools_annotate/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/bcftools/bcftools_annotate"
  executable: "target/nextflow/bcftools/bcftools_annotate/main.nf"
  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"
