name: "from_10xmtx_to_h5mu"
namespace: "convert"
scope: "public"
description: |
  Converts a 10x mtx into an h5mu file.
authors:
  - __merge__: /src/authors/robrecht_cannoodt.yaml
    roles: [ maintainer ]
arguments:
  - name: "--input"
    alternatives: ["-i"]
    type: file
    description: Input mtx folder
    example: input_dir_containing_gz_files
    direction: input
    required: true
  - name: "--output"
    alternatives: ["-o"]
    type: file
    description: Output h5mu file.
    example: output.h5mu
    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: run_test.py
  - path: /resources_test/pbmc_1k_protein_v3
engines:
  - type: docker
    image: python:3.11-slim
    setup:
      - type: apt
        packages: 
          - procps
      - type: python
        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
    __merge__: [ /src/base/requirements/python_test_setup.yaml ]
runners:
  - type: executable
  - type: nextflow
    directives:
      label: [lowmem, singlecpu]
