name: "bcl_convert"
version: "main"
authors:
- name: "Toni Verbeiren"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      github: "tverbeiren"
      linkedin: "verbeiren"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Data Scientist and CEO"
- name: "Dorien Roosen"
  roles:
  - "author"
  info:
    links:
      email: "dorien@data-intuitive.com"
      github: "dorien-er"
      linkedin: "dorien-roosen"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Data Scientist"
argument_groups:
- name: "Input arguments"
  arguments:
  - type: "file"
    name: "--bcl_input_directory"
    alternatives:
    - "-i"
    description: "Input run directory"
    info: null
    example:
    - "bcl_dir"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--sample_sheet"
    alternatives:
    - "-s"
    description: "Path to SampleSheet.csv file (default searched for in --bcl_input_directory)"
    info: null
    example:
    - "bcl_dir/sample_sheet.csv"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--run_info"
    description: "Path to RunInfo.xml file (default root of BCL input directory)"
    info: null
    example:
    - "bcl_dir/RunInfo.xml"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Lane and tile settings"
  arguments:
  - type: "integer"
    name: "--bcl_only_lane"
    description: "Convert only specified lane number (default all lanes)"
    info: null
    example:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--first_tile_only"
    description: "Only convert first tile of input (for testing & debugging)"
    info: null
    example:
    - true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--tiles"
    description: "Process only a subset of tiles by a regular expression"
    info: null
    example:
    - "s_[0-9]+_1"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--exclude_tiles"
    description: "Exclude set of tiles by a regular expression"
    info: null
    example:
    - "s_[0-9]+_1"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Resource arguments"
  arguments:
  - type: "boolean"
    name: "--shared_thread_odirect_output"
    description: "Use linux native asynchronous io (io_submit) for file output (Default=false)"
    info: null
    example:
    - true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--bcl_num_parallel_tiles"
    description: "\\# of tiles to process in parallel (default 1)"
    info: null
    example:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--bcl_num_conversion_threads"
    description: "\\# of threads for conversion (per tile, default # cpu threads)"
    info: null
    example:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--bcl_num_compression_threads"
    description: "\\# of threads for fastq.gz output compression (per tile, default\
      \ # cpu threads, or HW+12)"
    info: null
    example:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--bcl_num_decompression_threads"
    description: "\\# of threads for bcl/cbcl input decompression (per tile, default\
      \ half # cpu threads, or HW+8). Only applies when preloading files"
    info: null
    example:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Run arguments"
  arguments:
  - type: "boolean"
    name: "--bcl_only_matched_reads"
    description: "For pure BCL conversion, do not output files for 'Undetermined'\
      \ [unmatched] reads (output by default)"
    info: null
    example:
    - true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--no_lane_splitting"
    description: "Do not split FASTQ file by lane (false by default)"
    info: null
    example:
    - true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--num_unknown_barcodes_reported"
    description: "\\# of Top Unknown Barcodes to output (1000 by default)"
    info: null
    example:
    - 1000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--bcl_validate_sample_sheet_only"
    description: "Only validate RunInfo.xml & SampleSheet files (produce no FASTQ\
      \ files)"
    info: null
    example:
    - true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--strict_mode"
    description: "Abort if any files are missing (false by default)"
    info: null
    example:
    - true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--sample_name_column_enabled"
    description: "Use sample sheet 'Sample_Name' column when naming fastq files &\
      \ subdirectories"
    info: null
    example:
    - true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output arguments"
  arguments:
  - type: "file"
    name: "--output_directory"
    alternatives:
    - "-o"
    description: "Output directory containig fastq files"
    info: null
    example:
    - "fastq_dir"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--bcl_sampleproject_subdirectories"
    description: "Output to subdirectories based upon sample sheet 'Sample_Project'\
      \ column"
    info: null
    example:
    - true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--fastq_gzip_compression_level"
    description: "Set fastq output compression level 0-9 (default 1)"
    info: null
    example:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--reports"
    description: "Reports directory"
    info: null
    example:
    - "reports_dir"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--logs"
    description: "Reports directory"
    info: null
    example:
    - "logs_dir"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Convert bcl files to fastq files using bcl-convert.\nInformation about\
  \ upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\n\
  and [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
keywords:
- "demultiplex"
- "fastq"
- "bcl"
- "illumina"
license: "Proprietary"
links:
  repository: "https://github.com/viash-hub/biobox"
  homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html"
  documentation: "https://support.illumina.com/downloads/bcl-convert-user-guide.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: "debian:trixie-slim"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "apt"
    packages:
    - "wget"
    - "gdb"
    - "which"
    - "hostname"
    - "alien"
    - "procps"
    interactive: false
  - type: "docker"
    run:
    - "wget https://s3.amazonaws.com/webdata.illumina.com/downloads/software/bcl-convert/bcl-convert-4.2.7-2.el8.x86_64.rpm\
      \ -O /tmp/bcl-convert.rpm && \\\nalien -i /tmp/bcl-convert.rpm && \\\nrm -rf\
      \ /var/lib/apt/lists/* && \\\nrm /tmp/bcl-convert.rpm\n"
  - type: "docker"
    run:
    - "echo \"bcl-convert: \\\"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/\
      \ s/^bcl-convert\\ Version //p')\\\"\" > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/bcl_convert/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bcl_convert"
  executable: "target/executable/bcl_convert/bcl_convert"
  viash_version: "0.9.0"
  git_commit: "7f8bcc2b3e1ffaac9778b6acb42420b19660d1a1"
  git_remote: "https://x-access-token:ghs_aSDBedV4vU66pddFDN6d8UEy0ZQApn08RAsh@github.com/viash-hub/biobox"
  git_tag: "v0.2.0-3-g7f8bcc2"
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"