name: log1p
namespace: "transform"
scope: "public"
description: |
  Logarithmize the data matrix. Computes X = log(X + 1), where log denotes the natural logarithm unless a different base is given.
authors:
  - __merge__: /src/authors/dries_de_maeyer.yaml
    roles: [ maintainer ]
  - __merge__: /src/authors/robrecht_cannoodt.yaml
    roles: [ contributor ]
arguments:
  # input
  - 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: "--input_layer"
    type: string
    required: false
    description: "Input layer to use. If None, X is normalized"

  - name: "--output_layer"
    type: string
    description: Output layer to use. By default, use X.
    required: false

  # output
  - name: "--output"
    alternatives: ["-o"]
    type: file
    description: Output h5mu file.
    direction: output
    required: true
    default: output.h5mu

  # arguments
  - name: "--base"
    description: |
      Base of the logarithm. Natural logarithm is used by default.
    type: double
    example: 2

__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: run_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, /src/base/requirements/scanpy.yaml, .]
  test_setup:
    - type: python
      __merge__: [ /src/base/requirements/viashpy.yaml, .]

runners:
- type: executable
- type: nextflow
  directives:
    label: [midmem, lowcpu, highdisk]
