name: "samtools_stats"
namespace: "samtools"
version: "main"
authors:
- name: "Emma Rousseau"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      email: "emma@data-intuitive.com"
      github: "emmarousseau"
      linkedin: "emmarousseau1"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Bioinformatician"
argument_groups:
- name: "Inputs"
  arguments:
  - type: "file"
    name: "--input"
    description: "Input file.\n"
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bai"
    description: "Index file.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fasta"
    description: "Reference file the CRAM was created with.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--coverage"
    alternatives:
    - "-c"
    description: "Coverage distribution min;max;step. Default: [1, 1000, 1].\n"
    info: null
    example:
    - 1
    - 1000
    - 1
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--remove_dups"
    alternatives:
    - "-d"
    description: "Exclude from statistics reads marked as duplicates.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--customized_index_file"
    alternatives:
    - "-X"
    description: "Use a customized index file.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--required_flag"
    alternatives:
    - "-f"
    description: "Required flag, 0 for unset. See also `samtools flags`. Default:\
      \ `\"0\"`.\n"
    info: null
    example:
    - "0"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--filtering_flag"
    alternatives:
    - "-F"
    description: "Filtering flag, 0 for unset. See also `samtools flags`. Default:\
      \ `0`.\n"
    info: null
    example:
    - "0"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--GC_depth"
    description: "The size of GC-depth bins (decreasing bin size increases memory\
      \ requirement). Default: `20000`.\n"
    info: null
    example:
    - 20000.0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--insert_size"
    alternatives:
    - "-i"
    description: "Maximum insert size. Default: `8000`.\n"
    info: null
    example:
    - 8000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--id"
    alternatives:
    - "-I"
    description: "Include only listed read group or sample name.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--read_length"
    alternatives:
    - "-l"
    description: "Include in the statistics only reads with the given read length.\
      \ Default: `-1`.\n"
    info: null
    example:
    - -1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--most_inserts"
    alternatives:
    - "-m"
    description: "Report only the main part of inserts. Default: `0.99`.\n"
    info: null
    example:
    - 0.99
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--split_prefix"
    alternatives:
    - "-P"
    description: "Path or string prefix for filepaths output by --split (default is\
      \ input filename).\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--trim_quality"
    alternatives:
    - "-q"
    description: "The BWA trimming parameter. Default: `0`.\n"
    info: null
    example:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--ref_seq"
    alternatives:
    - "-r"
    description: "Reference sequence (required for GC-depth and mismatches-per-cycle\
      \ calculation).\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--split"
    alternatives:
    - "-S"
    description: "Also write statistics to separate files split by tagged field.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--target_regions"
    alternatives:
    - "-t"
    description: "Do stats in these regions only. Tab-delimited file chr,from,to,\
      \ 1-based, inclusive.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--sparse"
    alternatives:
    - "-x"
    description: "Suppress outputting IS rows where there are no insertions.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--remove_overlaps"
    alternatives:
    - "-p"
    description: "Remove overlaps of paired-end reads from coverage and base count\
      \ computations.\n"
    info: null
    direction: "input"
  - type: "integer"
    name: "--cov_threshold"
    alternatives:
    - "-g"
    description: "Only bases with coverage above this value will be included in the\
      \ target percentage computation. Default: `0`.\n"
    info: null
    example:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--input_fmt_option"
    description: "Specify a single input file format option in the form of OPTION\
      \ or OPTION=VALUE.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--reference"
    description: "Reference sequence FASTA FILE.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    alternatives:
    - "-o"
    description: "Output file.\n"
    info: null
    example:
    - "out.txt"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Reports alignment summary statistics for a BAM file."
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "test_data"
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
keywords:
- "statistics"
- "counts"
- "bam"
- "sam"
- "cram"
license: "MIT/Expat"
references:
  doi:
  - "10.1093/bioinformatics/btp352"
  - "10.1093/gigascience/giab008"
links:
  repository: "https://github.com/samtools/samtools"
  homepage: "https://www.htslib.org/"
  documentation: "https://www.htslib.org/doc/samtools-stats.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/samtools:1.19.2--h50ea8bc_1"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \\\nsed 's#Using\
      \ ##;s# \\([0-9\\.]*\\)$#: \\1#' > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/samtools/samtools_stats/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/samtools/samtools_stats"
  executable: "target/nextflow/samtools/samtools_stats/main.nf"
  viash_version: "0.9.0"
  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
  git_tag: "v0.2.0-27-g952ff08"
package_config:
  name: "biobox"
  version: "main"
  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 := '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"
