name: "runner"
version: "main"
argument_groups:
- name: "Input arguments"
  arguments:
  - type: "file"
    name: "--input"
    description: "Base directory of the canonical form `s3://<bucket>/<path>/<RunID>/`.\n\
      A tarball (tar.gz, .tgz, .tar) containing run information can be provided in\
      \ which\ncase the RunID is set to the name of the tarball without the extension.\n"
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--run_information"
    description: "CSV file containing sample information, which will be used as \n\
      input for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina)\n\
      or 'RunManifest.csv' (Element Biosciences). If not specified,\nwill try to autodetect\
      \ the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--demultiplexer"
    description: "Demultiplexer to use, choice depends on the provider\nof the instrument\
      \ that was used to generate the data.\nWhen not using --sample_sheet, specifying\
      \ this argument is not\nrequired.\n"
    info: null
    required: false
    choices:
    - "bases2fastq"
    - "bclconvert"
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Annotation flags"
  arguments:
  - type: "boolean_true"
    name: "--plain_output"
    description: "Flag to indicate that the output should be stored directly under\
      \ $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\n"
    info: null
    direction: "input"
- name: "Output arguments"
  arguments:
  - type: "file"
    name: "--fastq_output"
    info: null
    default:
    - "fastq"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--falco_output"
    info: null
    default:
    - "qc/fastqc"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--multiqc_output"
    info: null
    default:
    - "qc/multiqc_report.html"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--demultiplexer_logs"
    info: null
    default:
    - "demultiplexer_logs"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Other arguments"
  arguments:
  - type: "boolean_true"
    name: "--skip_copycomplete_check"
    description: "Disable the check for the presence of a \"CopyComplete.txt\" file\
      \ in input\ndirectory in case of Illumina data.\n"
    info: null
    direction: "input"
resources:
- type: "nextflow_script"
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
- type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
description: "Runner for demultiplexing of raw sequencing data"
info: null
status: "enabled"
scope:
  image: "public"
  target: "public"
requirements:
  commands:
  - "ps"
dependencies:
- name: "demultiplex"
  repository:
    type: "local"
- name: "io/publish"
  repository:
    type: "local"
license: "MIT"
links:
  repository: "https://github.com/viash-hub/demultiplex"
runners:
- type: "nextflow"
  id: "nextflow"
  directives:
    tag: "$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"
    script:
    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
engines:
- type: "native"
  id: "native"
- type: "native"
  id: "native"
build_info:
  config: "src/runner/config.vsh.yaml"
  runner: "nextflow"
  engine: "native|native"
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
  viash_version: "0.9.4"
  git_commit: "219bd5816e7e6a6c80b4d6f6c1d21b3ffe53c880"
  git_remote: "https://github.com/viash-hub/demultiplex"
  git_tag: "v0.1.1-30-g219bd58"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
package_config:
  name: "demultiplex"
  version: "main"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
    - path: "gs://viash-hub-resources/demultiplex/v3"
      dest: "testData"
  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main'"
  keywords:
  - "bioinformatics"
  - "sequence"
  - "demultiplexing"
  - "pipeline"
  license: "MIT"
  organization: "vsh"
  links:
    repository: "https://github.com/viash-hub/demultiplex"
    issue_tracker: "https://github.com/viash-hub/demultiplex/issues"