name: clear_slots
namespace: "transform"
scope: "public"
description: |
  Clear one or more AnnData slot containers from a modality in an h5mu file.

arguments:
  - name: "--input"
    alternatives: ["-i"]
    type: file
    description: Input h5mu file.
    direction: input
    required: true
    example: input.h5mu
  - name: "--modality"
    type: string
    description: Which modality from the input MuData file to process.
    default: "rna"
    required: false
  - name: "--slots"
    type: string
    multiple: true
    required: true
    choices: [obsm, varm, obsp, varp, uns, layers]
    description: |
      Names of the AnnData slot families to clear from the selected modality.
  - name: "--output"
    alternatives: ["-o"]
    type: file
    description: Output h5mu file.
    direction: output
    required: true
    default: output.h5mu
__merge__: [., /src/base/h5_compression_argument.yaml]

resources:
  - type: python_script
    path: script.py
  - path: /src/utils/setup_logger.py
  - path: /src/utils/compress_h5mu.py

test_resources:
  - type: python_script
    path: test.py
  - path: /resources_test/annotation_test_data/
  - 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: [singlecpu, lowmem]
