name: "cellranger_multi"
namespace: "workflows/ingestion"
scope: "public"
description: "A pipeline for running Cell Ranger multi."
info:
  name: Cell Ranger multi
  test_dependencies:
    - name: cellranger_multi_test
      namespace: test_workflows/ingestion
authors:
  - __merge__: /src/authors/dries_schaumont.yaml
    roles: [ author ]
__merge__: /src/mapping/cellranger_multi/cellranger_multi.yaml
argument_groups:
  - name: Outputs
    arguments:
      - name: "--output_raw"
        type: file
        direction: output
        description: "The raw output folder."
        required: true
        example: output_dir/
      - name: "--output_h5mu"
        type: file
        description: |
          Locations for the output files. Must contain a wildcard (*) character,
          which will be replaced with the sample name.
        example: "*.h5mu"
        direction: output
        required: true
      - name: "--uns_metrics"
        type: string
        description: Name of the .uns slot under which to QC metrics (if any).
        default: "metrics_cellranger"
dependencies:
  - name: mapping/cellranger_multi
    alias: cellranger_multi_component
  - name: convert/from_cellranger_multi_to_h5mu
resources:
  - type: nextflow_script
    path: main.nf
    entrypoint: run_wf
  - type: file
    path: /src/workflows/utils/
test_resources:
  - type: nextflow_script
    path: test.nf
    entrypoint: test_wf
  - type: nextflow_script
    path: test.nf
    entrypoint: test_wf2
  - path: /resources_test/10x_5k_anticmv/raw/
    dest: 10x_5k_anticmv/raw/
  - path: /resources_test/10x_5k_fixed/raw/
    dest: 10x_5k_fixed/raw/ 
  - path: /resources_test/reference_gencodev41_chr1
runners:
  - type: nextflow
