name: "gdo_singlesample"
namespace: "workflows/gdo"
scope: "public"
description: "Processing unimodal single-sample guide-derived oligonucleotide (GDO) data."
info:
  name: "GDO Singlesample"
  test_dependencies:
authors:
  - __merge__: /src/authors/dries_schaumont.yaml
    roles: [ author ]
argument_groups:
  - name: "Input"
    arguments:
      - name: "--id"
        required: true
        type: string
        description: ID of the sample.
        example: foo
      - name: "--input"
        type: file
        required: true
        description: Path to the sample.
        example: dataset.h5mu
      - name: "--layer"
        type: string
        required: false
        description: "Input layer to start from. By default, .X will be used."
  - name: "Output"
    arguments:
      - name: "--output"
        type: file
        required: true
        direction: output
        description: Destination path to the output.
        example: output.h5mu
  - name: "Filtering options"
    arguments:
      - name: "--min_counts"
        example: 200
        type: integer
        description: Minimum number of counts captured per cell.
      - name: "--max_counts"
        example: 5000000
        type: integer
        description: Maximum number of counts captured per cell.
  
      - name: "--min_guides_per_cell"
        type: integer
        example: 200
        description: Minimum of non-zero values per cell.
      - name: "--max_guides_per_cell"
        example: 1500000
        type: integer
        description: Maximum of non-zero values per cell.

      - name: "--min_cells_per_guide"
        example: 3
        type: integer
        description: Minimum of non-zero values per gene.

resources:
  - type: nextflow_script
    path: main.nf
    entrypoint: run_wf
  - type: file
    path: /src/workflows/utils/
dependencies:
  - name: filter/filter_with_counts
  - name: filter/do_filter
test_resources:
  - type: nextflow_script
    path: test.nf
    entrypoint: test_wf
  - path: /resources_test/10x_5k_lung_crispr
runners:
  - type: nextflow