task_template/src/data_processors/process_dataset/config.vsh.yaml at 8dbe23f5a416e6c635d98339c5e5f91617e2e878 · openproblems-bio/task_template · GitHub

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__merge__: ../../api/comp_data_processor.yaml
name: process_dataset
arguments:
  - name: "--method"
    type: "string"
    description: "The process method to assign train/test."
    choices: ["batch", "random"]
    default: "batch"
  - name: "--obs_label"
    type: "string"
    description: "Which .obs slot to use as label."
    default: "cell_type"
  - name: "--obs_batch"
    type: "string"
    description: "Which .obs slot to use as batch covariate."
    default: "batch"
  - name: "--seed"
    type: "integer"
    description: "A seed for the subsampling."
    example: 123
resources:
  - type: python_script
    path: script.py
  - path: /common/helper_functions/subset_h5ad_by_format.py

engines:
  - type: docker
    image: openproblems/base_python:1

runners:
  - type: executable
  - type: nextflow
    directives:
      label: [highmem, midcpu, midtime]