name: "samtools_sort"
namespace: "samtools"
version: "main"
authors:
- name: "Emma Rousseau"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      github: "emmarousseau"
      linkedin: "emmarousseau1"
argument_groups:
- name: "Inputs"
  arguments:
  - type: "file"
    name: "--input"
    description: "SAM/BAM/CRAM input file."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "Write final output to file.\n"
    info: null
    example:
    - "out.bam"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--output_fmt"
    alternatives:
    - "-O"
    description: "Specify output format (SAM, BAM, CRAM).\n"
    info: null
    example:
    - "BAM"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--output_fmt_option"
    description: "Specify a single output file format option in the form\nof 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
    example:
    - "ref.fa"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--write_index"
    description: "Automatically index the output files.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--prefix"
    alternatives:
    - "-T"
    description: "Write temporary files to PREFIX.nnnn.bam.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--no_PG"
    description: "Do not add a PG line.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--template_coordinate"
    description: "Sort by template-coordinate.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--input_fmt_option"
    description: "Specify a single input file format option in the form\nof OPTION\
      \ or OPTION=VALUE.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "integer"
    name: "--compression"
    alternatives:
    - "-l"
    description: "Set compression level, from 0 (uncompressed) to 9 (best).\n"
    info: null
    default:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--uncompressed"
    alternatives:
    - "-u"
    description: "Output uncompressed data (equivalent to --compression 0).\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--minimiser"
    alternatives:
    - "-M"
    description: "Use minimiser for clustering unaligned/unplaced reads.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--not_reverse"
    alternatives:
    - "-R"
    description: "Do not use reverse strand (only compatible with --minimiser)\n"
    info: null
    direction: "input"
  - type: "integer"
    name: "--kmer_size"
    alternatives:
    - "-K"
    description: "Kmer size to use for minimiser.\n"
    info: null
    example:
    - 20
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--order"
    alternatives:
    - "-I"
    description: "Order minimisers by their position in FILE FASTA.\n"
    info: null
    example:
    - "ref.fa"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--window"
    alternatives:
    - "-w"
    description: "Window size for minimiser INDEXING VIA --order REF.FA.\n"
    info: null
    example:
    - 100
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--homopolymers"
    alternatives:
    - "-H"
    description: "Squash homopolymers when computing minimiser.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--natural_sort"
    alternatives:
    - "-n"
    description: "Sort by read name (natural): cannot be used with samtools index.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--ascii_sort"
    alternatives:
    - "-N"
    description: "Sort by read name (ASCII): cannot be used with samtools index.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--tag"
    alternatives:
    - "-t"
    description: "Sort by value of TAG. Uses position as secondary index \n(or read\
      \ name if --natural_sort is set).\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Sort SAM/BAM/CRAM file."
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "test_data"
info: null
status: "enabled"
scope:
  image: "public"
  target: "public"
requirements:
  commands:
  - "ps"
keywords:
- "sort"
- "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-sort.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_sort/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/samtools/samtools_sort"
  executable: "target/executable/samtools/samtools_sort/samtools_sort"
  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"
