biobox/target/executable/bedtools/bedtools_annotate/.config.vsh.yaml

name: "bedtools_annotate"
namespace: "bedtools"
version: "v0.4.0"
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"
argument_groups:
- name: "Inputs"
  arguments:
  - type: "file"
    name: "--input"
    alternatives:
    - "-i"
    description: "Input file in BED, GFF, or VCF format to be annotated.\n\nEach interval\
      \ in this file will be analyzed for coverage by\nfeatures from the annotation\
      \ files.\n"
    info: null
    example:
    - "intervals.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--files"
    description: "One or more annotation files for coverage analysis.\n\n**Format:**\
      \ BED, GFF, or VCF files containing features to analyze\n**Multiple files:**\
      \ Use space-separated list or multiple --files flags\n**Processing:** Each file\
      \ analyzed separately with results in columns\n"
    info: null
    example:
    - "annotations1.bed"
    - "annotations2.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "Output file with annotation results.\n\nContains input intervals\
      \ with additional columns showing coverage\nstatistics from each annotation\
      \ file.\n"
    info: null
    example:
    - "annotated_intervals.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "string"
    name: "--names"
    description: "Descriptive names for each annotation file.\n\n**Usage:** One name\
      \ per file in same order as --files\n**Header:** Names appear in output header\
      \ line\n**Format:** Space-separated list or multiple --names flags\n"
    info: null
    example:
    - "ChIP-seq_peaks"
    - "DNA_methylation"
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--counts"
    description: "Report count of overlapping features instead of coverage fraction.\n\
      \n**Default output:** Fraction of input interval covered (0.0-1.0)\n**With --counts:**\
      \ Integer count of overlapping features\n**Use case:** When feature count is\
      \ more relevant than coverage area\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--both"
    description: "Report both feature counts and coverage fractions.\n\n**Output format:**\
      \ Count followed by fraction for each annotation file\n**Columns:** Doubles\
      \ the number of result columns\n**Use case:** Comprehensive analysis requiring\
      \ both metrics\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--strand"
    alternatives:
    - "-s"
    description: "Require same strandedness for overlap detection.\n\nOnly count overlaps\
      \ between features on the same strand.\nFeatures on opposite strands are ignored.\n\
      \n**Default:** Strand-agnostic analysis\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--different_strand"
    alternatives:
    - "-S"
    description: "Require different strandedness for overlap detection.\n\nOnly count\
      \ overlaps between features on opposite strands.\nFeatures on the same strand\
      \ are ignored.\n\n**Default:** Strand-agnostic analysis\n"
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Annotates the depth and breadth of coverage of features from multiple\
  \ files.\n\nThis tool analyzes how intervals in the input file are covered by features\n\
  from one or more annotation files. It reports either the fraction of each\ninterval\
  \ covered, the count of overlapping features, or both metrics.\n\n**Default behavior:**\
  \ Reports fraction of each input interval covered by features\n**Multiple files:**\
  \ Can process multiple annotation files simultaneously\n**Strand options:** Supports\
  \ same-strand, opposite-strand, or strand-agnostic analysis\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:
  - "bedtools"
  - "ps"
keywords:
- "Annotate"
- "Coverage"
- "Overlap"
- "BED"
- "GFF"
- "VCF"
license: "MIT"
references:
  doi:
  - "10.1093/bioinformatics/btq033"
links:
  repository: "https://github.com/arq5x/bedtools2"
  homepage: "https://bedtools.readthedocs.io/en/latest/"
  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/annotate.html"
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/bedtools:2.31.1--h13024bc_3"
  target_registry: "images.viash-hub.com"
  target_tag: "v0.4.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/bedtools/bedtools_annotate/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_annotate"
  executable: "target/executable/bedtools/bedtools_annotate/bedtools_annotate"
  viash_version: "0.9.4"
  git_commit: "666507c86de9150bfbdffdb2dbabc1dbde3c3262"
  git_remote: "https://github.com/viash-hub/biobox"
package_config:
  name: "biobox"
  version: "v0.4.0"
  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 := 'v0.4.0'"
  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"