name: delete_layer
namespace: "transform"
scope: "public"
description: |
  Delete an anndata layer from one or more modalities.
authors:
  - __merge__: /src/authors/dries_schaumont.yaml
    roles: [ maintainer ]
arguments:
  - name: "--input"
    alternatives: ["-i"]
    type: file
    description: Input h5mu file
    direction: input
    required: true
    example: input.h5mu
  - name: "--modality"
    description: |
      Which modality from the input MuData file to process.
    type: string
    default: "rna"
    required: false
  - name: "--layer"
    type: string
    required: true
    multiple: true
    description: "Input layer to remove"
  - name: "--output"
    alternatives: ["-o"]
    type: file
    description: Output h5mu file.
    direction: output
    required: true
    default: output.h5mu
  - name: "--missing_ok"
    type: boolean_true
    description: Do not raise an error if the layer does not exist for all modalities.
__merge__: [., /src/base/h5_compression_argument.yaml]

resources:
  - type: python_script
    path: script.py
  - path: /src/utils/compress_h5mu.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: [midmem, singlecpu]
