name: cellranger_multi
namespace: mapping
scope: "public"
description: Align fastq files using Cell Ranger multi.
authors:
  - __merge__: /src/authors/dries_schaumont.yaml
    roles: [ maintainer ]
  - __merge__: /src/authors/angela_pisco.yaml
    roles: [ author ]
  - __merge__: /src/authors/robrecht_cannoodt.yaml
    roles: [ author, maintainer ]
  - __merge__: /src/authors/dries_de_maeyer.yaml
    roles: [ author ]
  - __merge__: /src/authors/weiwei_schultz.yaml
    roles: [ contributor ]
  - __merge__: /src/authors/dorien_roosen.yaml
    roles: [ author ]
__merge__: /src/mapping/cellranger_multi/cellranger_multi.yaml
argument_groups:
  - name: Outputs
    arguments:
      - type: file
        name: --output
        direction: output
        description: The folder to store the alignment results.
        example: "/path/to/output"
        required: true

  - name: Executor arguments
    arguments:
      - name: "--dryrun"
        type: boolean_true
        description: "If true, the output directory will only contain the CWL input files, but the pipeline itself will not be executed."
resources:
  - type: python_script
    path: script.py
  - path: /src/utils/setup_logger.py
test_resources:
  - type: python_script
    path: test.py
  - path: /resources_test/10x_5k_anticmv/raw/
    dest: 10x_5k_anticmv/raw/
  - path: /resources_test/10x_5k_lung_crispr/raw/
    dest: 10x_5k_lung_crispr/raw/
  - path: /resources_test/10x_5k_beam/raw/
    dest: 10x_5k_beam/raw/
  - path: /resources_test/10x_5k_fixed/raw/
    dest: 10x_5k_fixed/raw 
  - path: /resources_test/10x_5k_beam/raw/ 
  - path: /resources_test/reference_gencodev41_chr1
engines:
  - type: docker
    image: quay.io/nf-core/cellranger:10.0.0
    setup:
      - type: apt
        packages:
          - procps
      - type: docker
        run: 
          - cellranger telemetry disable
      - type: python
        packages: 
          - pandas
          - pyyaml
    __merge__: [ /src/base/requirements/python_test_setup.yaml, .]
runners:
  - type: executable
  - type: nextflow
    directives:
      label: [ veryhighmem, highcpu, highdisk ]
