openpipeline/src/dataflow/move_anndata_slots/config.vsh.yaml at 9363de5b9fa05d75f1d49aea66207d515524c110 · openpipelines-bio/openpipeline · GitHub

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name: move_anndata_slots
namespace: "dataflow"
scope: "public"
description: |
  Move slots (.obs, .var, .obsm, .varm, .obsp, .varp, .uns) from a modality
  in a source MuData file into a modality in a target MuData file.
  The specified slots are copied from the source modality into the target
  modality, overwriting any existing data at those slots.

authors:
  - __merge__: /src/authors/jakub_majercik.yaml
    roles: [ author ]

argument_groups:
  - name: "Source"
    arguments:
      - name: "--input_source"
        type: file
        description: Source h5mu file to read slots from.
        direction: input
        required: true
        example: source.h5mu
      - name: "--source_modality"
        type: string
        description: Modality in the source h5mu file to read slots from.
        default: "rna"
        required: false

  - name: "Target"
    arguments:
      - name: "--input_target"
        type: file
        description: Target h5mu file to write slots into.
        direction: input
        required: true
        example: target.h5mu
      - name: "--target_modality"
        type: string
        description: |
          Modality in the target h5mu file to write slots into.
          Defaults to the value of --source_modality.
        required: false

  - name: "Slots to move"
    arguments:
      - name: "--obs"
        type: string
        description: |
          Column names from .obs to move from the source modality to the
          target modality. If not provided, .obs is not moved.
        multiple: true
        required: false
      - name: "--var"
        type: string
        description: |
          Column names from .var to move from the source modality to the
          target modality. If not provided, .var is not moved.
        multiple: true
        required: false
      - name: "--obsm"
        type: string
        description: |
          Keys from .obsm to move from the source modality to the target
          modality. If not provided, .obsm is not moved.
        multiple: true
        required: false
      - name: "--varm"
        type: string
        description: |
          Keys from .varm to move from the source modality to the target
          modality. If not provided, .varm is not moved.
        multiple: true
        required: false
      - name: "--obsp"
        type: string
        description: |
          Keys from .obsp to move from the source modality to the target
          modality. If not provided, .obsp is not moved.
        multiple: true
        required: false
      - name: "--varp"
        type: string
        description: |
          Keys from .varp to move from the source modality to the target
          modality. If not provided, .varp is not moved.
        multiple: true
        required: false
      - name: "--uns"
        type: string
        description: |
          Keys from .uns to move from the source modality to the target
          modality. If not provided, .uns is not moved.
        multiple: true
        required: false

  - name: "Options"
    arguments:
      - name: "--allow_overwrite"
        type: boolean_true
        description: |
          Allow overwriting keys that already exist in the target modality.
          By default, the component raises an error if a key already exists.
          When enabled, existing keys are overwritten with a warning.

  - name: "Output"
    arguments:
      - name: "--output"
        alternatives: ["-o"]
        type: file
        description: Output h5mu file (the target with slots added from the source).
        direction: output
        required: true
        example: 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

engines:
  - type: docker
    image: python:3.13-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 ]