name: bcl_convert
namespace: demux
scope: "public"
description: |
  Convert bcl files to fastq files using bcl-convert.
  Information about upgrading from bcl2fastq via
  https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html
  and https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html
authors:
  - __merge__: /src/authors/toni_verbeiren.yaml
    roles: [ author, maintainer ]
  - __merge__: /src/authors/marijke_van_moerbeke.yaml
    roles: [ author ]
  - __merge__: /src/authors/weiwei_schultz.yaml
    roles: [ contributor ]
  - __merge__: /src/authors/dorien_roosen.yaml
    roles: [ author ]
arguments:
  - name: "--input"
    alternatives: [ "-i" ]
    type: file
    required: true
    description: Input run directory
    example: bcl_dir
  - name: "--sample_sheet"
    alternatives: [ "-s" ]
    type: file
    required: true
    description: Pointer to the sample sheet
    example: bcl_dir
  - name: "--output"
    alternatives: [ "-o" ]
    type: file
    direction: output
    required: true
    description: Output directory containig fastq files
    example: fastq_dir
  - name: "--reports"
    type: file
    direction: output
    required: false
    description: Reports directory
    example: reports_dir
  - name: "--test_mode"
    type: boolean
    default: false
    description: Should bcl-convert be run in test mode (using --first-tile-only)?
  - name: "--strict_mode"
    type: boolean
    default: false
    description: Abort if any files are missing.
  - name: "--tiles"
    type: string
    required: false
    description: Process only a subset of tiles by a regular expression.
  - name: "--exclude_tiles"
    type: string
    required: false
    description: "Exclude set of tiles by a regular expression"
  - name: --no_lane_splitting
    type: boolean
    required: false
    description: Wheter to avoid splitting FASTQ file by lane. 
  
resources:
  - type: bash_script
    path: script.sh
test_resources:
  - type: bash_script
    path: test.sh
  - path: /resources_test/cellranger_tiny_bcl/bcl2

engines:
- type: docker
  image: ghcr.io/data-intuitive/bclconvert:4.2
  setup:
    - type: apt
      packages:
        - procps

runners:
- type: executable
- type: nextflow
  directives:
    label: [ midmem, midcpu ]
