name: "bedtools_genomecov"
namespace: "bedtools"
version: "main"
authors:
- name: "Theodoro Gasperin Terra Camargo"
  roles:
  - "author"
  info:
    links:
      email: "theodorogtc@gmail.com"
      github: "tgaspe"
      linkedin: "theodoro-gasperin-terra-camargo"
- 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 genomic intervals file in BED, GFF, or VCF format.\n\n**Supported\
      \ formats:**\n- BED format (standard genomic intervals)\n- GFF/GTF format (gene\
      \ annotations)\n- VCF format (variant calls)\n\n**Note:** Required when not\
      \ using `--input_bam`\n"
    info: null
    example:
    - "input.bed"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--input_bam"
    alternatives:
    - "-ibam"
    description: "Input BAM file for coverage calculation.\n\n**Requirements:**\n\
      - BAM file must be sorted by position\n- When using BAM input, `--genome` option\
      \ is ignored\n- Coordinates are determined from BAM header\n"
    info: null
    example:
    - "input.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome"
    alternatives:
    - "-g"
    description: "Genome file defining chromosome names and sizes.\n\n**Format:**\
      \ Two-column tab-delimited file:\n```\nchr1    248956422\nchr2    242193529\n\
      ```\n\n**Note:** Required when using `--input`, ignored when using `--input_bam`\n"
    info: null
    example:
    - "genome.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "Output file containing coverage information.\n\n**Output formats\
      \ depend on options:**\n- **Default:** Coverage histogram (depth vs count)\n\
      - **With `--depth`:** Per-base depth (1-based coordinates)\n- **With `--bed_graph`:**\
      \ BedGraph format for genome browsers\n"
    info: null
    example:
    - "coverage.txt"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "boolean_true"
    name: "--depth"
    alternatives:
    - "-d"
    description: "Report the depth at each genome position with 1-based coordinates.\n\
      \n**Output format:** `chromosome position depth`\n\n**Default behavior:** Reports\
      \ coverage histogram instead\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--depth_zero"
    alternatives:
    - "-dz"
    description: "Report depth at each genome position with 0-based coordinates.\n\
      \n**Features:**\n- Only reports positions with non-zero coverage\n- Uses 0-based\
      \ coordinate system\n- More memory efficient than `--depth`\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--bed_graph"
    alternatives:
    - "-bg"
    description: "Report depth in BedGraph format for genome browser visualization.\n\
      \n**Output format:** `chromosome start end depth`\n\nSee [BedGraph specification](https://genome.ucsc.edu/goldenPath/help/bedgraph.html)\
      \ for details.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--bed_graph_zero_coverage"
    alternatives:
    - "-bga"
    description: "Report depth in BedGraph format including zero-coverage regions.\n\
      \n**Features:**\n- Same as `--bed_graph` but includes regions with 0 coverage\n\
      - Useful for finding uncovered regions: `grep -w 0$ output.bg`\n- Generates\
      \ larger output files\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--split"
    description: "Treat \"split\" BAM or BED12 entries as distinct BED intervals.\n\
      when computing coverage.\nFor BAM files, this uses the CIGAR \"N\" and \"D\"\
      \ operations \nto infer the blocks for computing coverage.\nFor BED12 files,\
      \ this uses the BlockCount, BlockStarts, and BlockEnds\nfields (i.e., columns\
      \ 10,11,12).\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--ignore_deletion"
    alternatives:
    - "-ignoreD"
    description: "Ignore local deletions (CIGAR \"D\" operations) in BAM entries\n\
      when computing coverage.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--strand"
    description: "Calculate coverage of intervals from a specific strand.\nWith BED\
      \ files, requires at least 6 columns (strand is column 6). \n"
    info: null
    required: false
    choices:
    - "+"
    - "-"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--pair_end_coverage"
    alternatives:
    - "-pc"
    description: "Calculate coverage of pair-end fragments.\nWorks for BAM files only\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--fragment_size"
    alternatives:
    - "-fs"
    description: "Force to use provided fragment size instead of read length\nWorks\
      \ for BAM files only\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--du"
    description: "Change strand af the mate read (so both reads from the same strand)\
      \ useful for strand specific\nWorks for BAM files only\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--five_prime"
    alternatives:
    - "-5"
    description: "Calculate coverage of 5\" positions (instead of entire interval).\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--three_prime"
    alternatives:
    - "-3"
    description: "Calculate coverage of 3\" positions (instead of entire interval).\n"
    info: null
    direction: "input"
  - type: "integer"
    name: "--max"
    description: "Combine all positions with a depth >= max into\na single bin in\
      \ the histogram. Irrelevant\nfor -d and -bedGraph\n- (INTEGER)\n"
    info: null
    required: false
    min: 0
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--scale"
    description: "Scale the coverage by a constant factor.\nEach coverage value is\
      \ multiplied by this factor before being reported.\nUseful for normalizing coverage\
      \ by, e.g., reads per million (RPM).\n- Default is 1.0; i.e., unscaled.\n- (FLOAT)\n"
    info: null
    required: false
    min: 0.0
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--trackline"
    description: "Adds a UCSC/Genome-Browser track line definition in the first line\
      \ of the output.\n- See here for more details about track line definition:\n\
      \      http://genome.ucsc.edu/goldenPath/help/bedgraph.html\n- NOTE: When adding\
      \ a trackline definition, the output BedGraph can be easily\n      uploaded\
      \ to the Genome Browser as a custom track,\n      BUT CAN NOT be converted into\
      \ a BigWig file (w/o removing the first line).\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--trackopts"
    description: "Writes additional track line definition parameters in the first\
      \ line.\n- Example:\n  -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'\n\
      \  Note the use of single-quotes if you have spaces in your parameters.\n- (TEXT)\n"
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Compute the coverage of a feature file among a genome.\n\nCalculates\
  \ genome-wide coverage statistics from BED, GFF, VCF, or BAM files.\nCan produce\
  \ coverage histograms, per-base depth, or BedGraph format output.\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:
- "genome coverage"
- "BED"
- "GFF"
- "VCF"
- "BAM"
- "depth"
- "histogram"
- "bedgraph"
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/genomecov.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: "main"
  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_genomecov/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_genomecov"
  executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
  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"
