name: "from_bdrhap_to_h5mu"
namespace: "convert"
scope: "public"
description: |
  Convert the output of a BD Rhapsody pipeline v2.x to a MuData h5 file.
authors:
  - __merge__: /src/authors/dorien_roosen.yaml
    roles: [ author, maintainer ]
  - __merge__: /src/authors/robrecht_cannoodt.yaml
    roles: [ author ]
argument_groups:
  - name: Inputs
    arguments:
      - name: "--id"
        type: string
        description: "A sample ID."
        example: my_id
        required: true
      - name: "--input"
        alternatives: [-i]
        type: file
        description: The output h5mu of a BD Rhapsody workflow.
        required: true
        example: sample.h5mu
  - name: Outputs
    arguments:
      - name: "--output"
        alternatives: [-o]
        direction: output
        type: file
        description: "Output h5mu file."
        required: true
        example: output.h5mu
__merge__: [., /src/base/h5_compression_argument.yaml]

resources:
  - type: python_script
    path: script.py
test_resources:
  - type: python_script
    path: test.py
  - path: /resources_test/bdrhap_5kjrt/processed/output_raw/sample.h5mu
engines:
  - type: docker
    image: python:3.11-slim
    setup:
      - type: apt
        packages:
          - procps
      - type: python
        __merge__: /src/base/requirements/anndata_mudata.yaml
runners:
  - type: executable
  - type: nextflow
    directives:
      label: [lowmem, singlecpu]
