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

name: "bedtools_coverage"
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_a"
    alternatives:
    - "-a"
    description: "Query intervals file in BED, GFF, or VCF format.\n\n**Purpose:**\
      \ Intervals for which coverage will be calculated\n**BED format:** Standard\
      \ genomic interval format\n**GFF format:** Gene feature format with annotations\n\
      **VCF format:** Variant call format\n"
    info: null
    example:
    - "target_regions.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--input_b"
    alternatives:
    - "-b"
    description: "Coverage source file(s) in BED, GFF, VCF, or BAM format.\n\n**Purpose:**\
      \ Features that provide coverage over query intervals\n**Multiple files:** Can\
      \ specify multiple coverage sources\n**BAM support:** Binary alignment files\
      \ for sequencing coverage\n"
    info: null
    example:
    - "alignments.bam"
    - "features.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 coverage statistics.\n\n**Default output:** For\
      \ each interval in A, reports:\n1. Number of overlapping features from B\n2.\
      \ Number of bases in A with non-zero coverage\n3. Length of interval in A\n\
      4. Fraction of bases in A with non-zero coverage\n"
    info: null
    example:
    - "coverage_stats.txt"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Coverage Reporting"
  arguments:
  - type: "boolean_true"
    name: "--histogram"
    alternatives:
    - "-hist"
    description: "Report coverage histogram for each feature and summary.\n\n**Output\
      \ format:** depth, bases at depth, feature size, percentage\n**Use case:** Detailed\
      \ coverage distribution analysis\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--depth_per_position"
    alternatives:
    - "-d"
    description: "Report depth at each position in each interval.\n\n**Output:** One-based\
      \ positions with coverage depth\n**Use case:** Position-specific coverage analysis\n\
      **Note:** Generates large output for long intervals\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--counts_only"
    alternatives:
    - "-counts"
    description: "Only report overlap counts, no fractions.\n\n**Simplified output:**\
      \ Just the number of overlapping features\n**Use case:** When only overlap counts\
      \ are needed\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--mean_depth"
    alternatives:
    - "-mean"
    description: "Report mean coverage depth for each interval.\n\n**Output:** Average\
      \ depth across all positions in interval\n**Use case:** Summary coverage statistics\n"
    info: null
    direction: "input"
- name: "Strand Options"
  arguments:
  - type: "boolean_true"
    name: "--same_strand"
    alternatives:
    - "-s"
    description: "Require same strandedness for overlaps.\n\n**Default:** Overlaps\
      \ reported regardless of strand\n**When enabled:** Only count overlaps on same\
      \ strand\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--different_strand"
    alternatives:
    - "-S"
    description: "Require different strandedness for overlaps.\n\n**Default:** Overlaps\
      \ reported regardless of strand\n**When enabled:** Only count overlaps on opposite\
      \ strand\n"
    info: null
    direction: "input"
- name: "Overlap Requirements"
  arguments:
  - type: "double"
    name: "--min_overlap_a"
    alternatives:
    - "-f"
    description: "Minimum overlap required as fraction of A.\n\n**Range:** 0.0 to\
      \ 1.0\n**Default:** 1E-9 (essentially 1bp)\n**Example:** 0.50 requires 50% of\
      \ A to be overlapped\n"
    info: null
    example:
    - 0.5
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--min_overlap_b"
    alternatives:
    - "-F"
    description: "Minimum overlap required as fraction of B.\n\n**Range:** 0.0 to\
      \ 1.0\n**Default:** 1E-9 (essentially 1bp)\n**Example:** 0.80 requires 80% of\
      \ B to overlap A\n"
    info: null
    example:
    - 0.8
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--reciprocal"
    alternatives:
    - "-r"
    description: "Require reciprocal minimum fraction for A AND B.\n\n**Requires:**\
      \ Both -f and -F fractions to be satisfied\n**Use case:** Stringent overlap\
      \ requirements\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--either"
    alternatives:
    - "-e"
    description: "Require minimum fraction for A OR B (not both).\n\n**Default:**\
      \ Both -f and -F must be satisfied\n**When enabled:** Either fraction requirement\
      \ is sufficient\n"
    info: null
    direction: "input"
- name: "Format Options"
  arguments:
  - type: "boolean_true"
    name: "--split"
    description: "Treat split BAM/BED12 entries as distinct intervals.\n\n**BAM:**\
      \ Handle spliced alignments as separate blocks\n**BED12:** Process each block\
      \ independently\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--bed_output"
    alternatives:
    - "-bed"
    description: "Write output in BED format when using BAM input.\n\n**Default:**\
      \ BAM input produces BAM-style output\n**When enabled:** Force BED format output\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--header"
    description: "Print header from input A file before results.\n\n**Use case:**\
      \ Preserve metadata from input file\n"
    info: null
    direction: "input"
- name: "Performance Options"
  arguments:
  - type: "boolean_true"
    name: "--sorted"
    description: "Use chromsweep algorithm for sorted input.\n\n**Requirements:**\
      \ Input must be sorted by chromosome and position\n**Performance:** Faster processing\
      \ for large files\n"
    info: null
    direction: "input"
  - type: "file"
    name: "--genome"
    alternatives:
    - "-g"
    description: "Genome file for consistent chromosome ordering.\n\n**Format:** Tab-delimited\
      \ chromosome names and sizes\n**Use case:** Ensure consistent sort order with\
      \ -sorted option\n"
    info: null
    example:
    - "genome.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--no_name_check"
    alternatives:
    - "-nonamecheck"
    description: "Don't error on different chromosome naming conventions.\n\n**Example:**\
      \ Allows mixing \"chr1\" and \"chr01\"\n**Use case:** Working with files from\
      \ different sources\n"
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Calculate coverage of genomic intervals from one file over intervals\
  \ in another.\n\nThis tool reports the depth and breadth of coverage of features\
  \ from file B\nover the intervals in file A. It provides detailed coverage statistics\
  \ including\noverlap counts, covered bases, and coverage fractions.\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:
- "genomics"
- "intervals"
- "coverage"
- "depth"
- "breadth"
- "overlap"
- "statistics"
license: "MIT"
references:
  doi:
  - "10.1093/bioinformatics/btq033"
links:
  repository: "https://github.com/arq5x/bedtools2"
  homepage: "https://bedtools.readthedocs.io/"
  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/coverage.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\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/bedtools/bedtools_coverage/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_coverage"
  executable: "target/executable/bedtools/bedtools_coverage/bedtools_coverage"
  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"