name: from_h5mu_to_h5ad
namespace: "convert"
scope: "public"
description: |
  Converts a h5mu file into a h5ad file.
authors:
  - __merge__: /src/authors/robrecht_cannoodt.yaml
    roles: [ maintainer ]
arguments:
  - name: "--input"
    alternatives: ["-i"]
    type: file
    description: Input MuData file
    default: input.h5mu
    direction: input
    required: true
  - name: "--modality"
    description: |
      Which modality from the input MuData file to process.
    type: string
    default: "rna"
    required: false
  - name: "--output"
    alternatives: ["-o"]
    type: file
    description: Output AnnData file.
    default: output.h5ad
    direction: output
__merge__: [., /src/base/h5_compression_argument.yaml]


resources:
  - type: python_script
    path: script.py
  - path: /src/utils/setup_logger.py
test_resources:
  - type: python_script
    path: test.py
  - path: /resources_test/pbmc_1k_protein_v3

engines:
- type: docker
  image: python:3.12-slim
  setup:
    - type: apt
      packages: 
        - procps
    - type: python
      __merge__: [/src/base/requirements/anndata_mudata.yaml]
  __merge__: [ /src/base/requirements/python_test_setup.yaml, . ]

runners:
- type: executable
- type: nextflow
  directives:
    label: [lowmem, singlecpu]
