name: "bases2fastq"
version: "main"
authors:
- name: "Dries Schaumont"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      email: "dries@data-intuitive.com"
      github: "DriesSchaumont"
      orcid: "0000-0002-4389-0440"
      linkedin: "dries-schaumont"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Data Scientist"
argument_groups:
- name: "Input"
  arguments:
  - type: "file"
    name: "--analysis_directory"
    description: "Location of analysis directory"
    info: null
    example:
    - "input"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--run_manifest"
    alternatives:
    - "-r"
    description: "Location of run manifest to use instead of default RunManifest.csv\
      \ found in analysis directory"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--output_directory"
    alternatives:
    - "-o"
    description: "Location to save output fastqs"
    info: null
    example:
    - "fastq_dir"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--report"
    description: "Output location for the HTML report"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--logs"
    description: "Directory containing log files"
    info: null
    example:
    - "logs_dir"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Arguments"
  arguments:
  - type: "string"
    name: "--chemistry_version"
    description: "Run parameters override, chemistry version."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--demux_only"
    alternatives:
    - "-d"
    description: "Generate demux files and indexing stats without generating FASTQ\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--detect_adapters"
    description: "Detect adapters sequences, overriding any sequences present in run\
      \ manifest.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--error_on_missing"
    description: "Terminate execution for a missing file (by default, missing files\
      \ are\nskipped and execution continues). Also set by --strict.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--exclude_tile"
    alternatives:
    - "-e"
    description: "Regex matching tile names to exclude. This flag can be specified\
      \ multiple times. (e.g. L1.*C0[23]S.)\n"
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--filter_mask"
    description: "Run parameters override, custom pass filter mask.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--flowcell_id"
    description: "Run parameters override, flowcell ID.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--force_index_orientation"
    description: "Do not attempt to find orientation for I1/I2 reads (reverse complement).\n\
      Use orientation given in run manifest.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--group_fastq"
    description: "Group all FASTQ/stats/metrics for a project are in the project folder.\n"
    info: null
    direction: "input"
  - type: "integer"
    name: "--i1_cycles"
    description: "Run parameters override, I1 cycles.\n"
    info: null
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--i2_cycles"
    description: "Run parameters override, I2 cycles\n"
    info: null
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--include_tile"
    alternatives:
    - "-i"
    description: "Regex matching tile names to include. This flag\ncan be specified\
      \ multiple times. (e.g. L1.*C0[23]S.)\n"
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--kit_configuration"
    description: "Run parameters override, kit configuration.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--legacy_fastq"
    description: "Legacy naming for FASTQ files (e.g. SampleName_S1_L001_R1_001.fastq.gz)\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--log_level"
    alternatives:
    - "-l"
    description: "Severity level for logging.\n"
    info: null
    example:
    - "INFO"
    required: false
    choices:
    - "DEBUG"
    - "INFO"
    - "WARNING"
    - "ERROR"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--no_error_on_invalid"
    description: "Skip invalid files and continue execution. Overridden by --strict\
      \ options\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_projects"
    description: "Disable project directories\n"
    info: null
    direction: "input"
  - type: "integer"
    name: "--num_unassigned"
    description: "Max Number of unassigned sequences to report.\n"
    info: null
    example:
    - 30
    required: false
    min: 0
    max: 1000
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--preparation_workflow"
    description: "Run parameters override, preparation workflow. \n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--qc_only"
    description: "Quickly generate run stats for single tile without generating FASTQ.\n\
      Use --include_tile/--exclude_tile to define custom tile set.\n"
    info: null
    direction: "input"
  - type: "integer"
    name: "--r1_cycles"
    description: "Run parameters override, R1 cycles.\n"
    info: null
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--r2_cycles"
    description: "Run parameters override, R2 cycles.\n"
    info: null
    required: false
    min: 1
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--split_lanes"
    description: "Split FASTQ files by lane.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--skip_qc_report"
    description: "Do not generate HTML QC report.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--skip_multi_qc"
    description: "Do not generate MultiQC HTML report.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--settings"
    description: "Run manifest settings override. This option may be specified multiple\
      \ times.\n"
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Cyto-fastq Arguments"
  arguments:
  - type: "string"
    name: "--batch"
    description: "Restrict cyto-fastq generation to batch(es) that match comma delimited\
      \ list (e.g. --batch B01,B02,B03).\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--cyto_fastq_mask"
    description: "Cycle mask for cyto fastq generation. This flag can be specified\
      \ multiple times.\n"
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--panel"
    description: "Local or remote path to panel JSON\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--per_target_fastq"
    description: "Create per-target fastq for each cell assignment target site in\
      \ each DISS batch according to FastqMasks in TargetCellAssignmentManifest.\n"
    info: null
    direction: "input"
  - type: "file"
    name: "--tca_manifest"
    description: "Location of TargetCellAssignmentManifest to use instead of default\
      \ csv found in analysis directory\n"
    info: null
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Bases2Fastq demultiplexes sequencing data generated by Element Biosciences\
  \ instruments and converts base calls into FASTQ files.\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "test_helpers.sh"
info: null
status: "enabled"
scope:
  image: "public"
  target: "public"
requirements:
  commands:
  - "bases2fastq"
  - "ps"
keywords:
- "demultiplex"
- "fastq"
- "demux"
- "Element Biosciences"
license: "Proprietary"
links:
  repository: "https://github.com/Illumina/bases2fastq"
  homepage: "https://www.elembio.com/"
  documentation: "https://docs.elembio.io/docs/bases2fastq/introduction/"
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: "elembio/bases2fastq:2.2.1"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "bases2fastq --version 2>&1 | head -1 | sed 's/.*version \\([0-9\\\\.]*\\).*/bases2fastq:\
      \ \\1/' > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/bases2fastq/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/bases2fastq"
  executable: "target/nextflow/bases2fastq/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"
