name: cellranger_mkfastq
namespace: demux
scope: "public"
description: Demultiplex raw sequencing data
usage: |
  cellranger_mkfastq \
    --input /path/to/bcl \
    --sample_sheet SampleSheet.csv \
    --output /path/to/output
authors:
  - __merge__: /src/authors/angela_pisco.yaml
    roles: [ author ]
  - __merge__: /src/authors/samuel_d_souza.yaml
    roles: [ author ]
  - __merge__: /src/authors/robrecht_cannoodt.yaml
    roles: [ author, maintainer ]
arguments:
  - type: file
    name: --input
    description: Path to the (untarred) BCL files. Expects 'RunParameters.xml' at './'.
    example: /path/to/bcl
    required: true
  - type: file
    name: --sample_sheet
    description: The path to the sample sheet.
    example: SampleSheet.csv
    required: true
  - type: file
    name: --output
    direction: output
    description: The folder to store the demux results
    example: "/path/to/output"
    default: fastqs
    required: true
  - name: "--reports"
    type: file
    direction: output
    required: false
    description: Reports directory
    example: reports_dir
resources:
  - type: bash_script
    path: script.sh
  - path: /src/utils/setup_logger.py
test_resources:
  - type: python_script
    path: test.py
  - path: /resources_test/cellranger_tiny_bcl

engines:
- type: docker
  image: ghcr.io/data-intuitive/cellranger:9.0
  setup:
    - type: docker
      run: |
        DEBIAN_FRONTEND=noninteractive apt update && \
        apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/*
  test_setup:
    - type: python
      __merge__: [ /src/base/requirements/viashpy.yaml, .]

runners:
- type: executable
- type: nextflow
  directives:
    label: [ highmem, highcpu ]
