name: "bbmap_bbsplit"
namespace: "bbmap"
version: "main"
argument_groups:
- name: "Input"
  arguments:
  - type: "string"
    name: "--id"
    description: "Sample ID"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--paired"
    description: "Paired fastq files or not?"
    info: null
    direction: "input"
  - type: "file"
    name: "--input"
    description: "Input fastq files, either one or two (paired), separated by \";\"\
      ."
    info: null
    example:
    - "reads.fastq"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--ref"
    description: "Reference FASTA files, separated by \";\". The primary reference\
      \ should be specified first."
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--only_build_index"
    description: "If set, only builds the index. Otherwise, mapping is performed."
    info: null
    direction: "input"
  - type: "file"
    name: "--build"
    description: "Index to be used for mapping. \n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--qin"
    description: "Set to 33 or 64 to specify input quality value ASCII offset. Automatically\
      \ detected if\nnot specified.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--interleaved"
    description: "True forces paired/interleaved input; false forces single-ended\
      \ mapping.\nIf not specified, interleaved status will be autodetected from read\
      \ names.\n"
    info: null
    direction: "input"
  - type: "integer"
    name: "--maxindel"
    description: "Don't look for indels longer than this. Lower is faster. Set to\
      \ >=100k for RNA-seq.\n"
    info: null
    example:
    - 20
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--minratio"
    description: "Fraction of max alignment score required to keep a site. Higher\
      \ is faster.\n"
    info: null
    example:
    - 0.56
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--minhits"
    description: "Minimum number of seed hits required for candidate sites. Higher\
      \ is faster.\n"
    info: null
    example:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--ambiguous"
    description: "Set behavior on ambiguously-mapped reads (with multiple top-scoring\
      \ mapping locations).\n  * best    Use the first best site (Default)\n  * toss\
      \    Consider unmapped\n  * random  Select one top-scoring site randomly\n \
      \ * all     Retain all top-scoring sites.  Does not work yet with SAM output\n"
    info: null
    example:
    - "best"
    required: false
    choices:
    - "best"
    - "toss"
    - "random"
    - "all"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--ambiguous2"
    description: "Set behavior only for reads that map ambiguously to multiple different\
      \ references.\nNormal 'ambiguous=' controls behavior on all ambiguous reads;\n\
      Ambiguous2 excludes reads that map ambiguously within a single reference.\n\
      \  * best    Use the first best site (Default)\n  * toss    Consider unmapped\n\
      \  * all     Write a copy to the output for each reference to which it maps\n\
      \  * split   Write a copy to the AMBIGUOUS_ output for each reference to which\
      \ it maps\n"
    info: null
    example:
    - "best"
    required: false
    choices:
    - "best"
    - "toss"
    - "all"
    - "split"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--qtrim"
    description: "Quality-trim ends to Q5 before mapping. Options are 'l' (left),\
      \ 'r' (right), and 'lr' (both).\n"
    info: null
    required: false
    choices:
    - "l"
    - "r"
    - "lr"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--untrim"
    description: "Undo trimming after mapping. Untrimmed bases will be soft-clipped\
      \ in cigar strings."
    info: null
    direction: "input"
- name: "Output"
  arguments:
  - type: "file"
    name: "--index"
    description: "Location to write the index.\n"
    info: null
    example:
    - "BBSplit_index"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fastq_1"
    description: "Output file for read 1.\n"
    info: null
    example:
    - "read_out1.fastq"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--fastq_2"
    description: "Output file for read 2.\n"
    info: null
    example:
    - "read_out2.fastq"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--sam2bam"
    alternatives:
    - "--bs"
    description: "Write a shell script to 'file' that will turn the sam output into\
      \ a sorted, indexed bam file.\n"
    info: null
    example:
    - "script.sh"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--scafstats"
    description: "Write statistics on how many reads mapped to which scaffold to this\
      \ file.\n"
    info: null
    example:
    - "scaffold_stats.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--refstats"
    description: "Write statistics on how many reads were assigned to which reference\
      \ to this file.\nUnmapped reads whose mate mapped to a reference are considered\
      \ assigned and will be counted.\n"
    info: null
    example:
    - "reference_stats.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--nzo"
    description: "Only print lines with nonzero coverage."
    info: null
    direction: "input"
  - type: "string"
    name: "--bbmap_args"
    description: "Additional arguments from BBMap to pass to BBSplit.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Split sequencing reads by mapping them to multiple references simultaneously."
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
info: null
status: "enabled"
scope:
  image: "public"
  target: "public"
requirements:
  commands:
  - "ps"
license: "BBTools Copyright (c) 2014"
links:
  repository: "https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh"
  homepage: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/"
  documentation: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbmap-guide/"
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: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "apt-get update && \\\napt-get install -y build-essential openjdk-17-jdk wget\
      \ tar && \\\nwget --no-check-certificate https://sourceforge.net/projects/bbmap/files/BBMap_39.01.tar.gz\
      \ && \\\ntar xzf BBMap_39.01.tar.gz && \\\ncp -r bbmap/* /usr/local/bin\n"
  - type: "docker"
    run:
    - "bbsplit.sh --version 2>&1 | awk '/BBMap version/{print \"BBMAP:\", $NF}' >\
      \ /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/bbmap/bbmap_bbsplit/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/bbmap/bbmap_bbsplit"
  executable: "target/nextflow/bbmap/bbmap_bbsplit/main.nf"
  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"
