task_ist_preprocessing/src/methods_segmentation/scs_segmentation/config.vsh.yaml at 1b10a6a6d55e67c4e8cb897a026b639f0ee1f68d · openproblems-bio/task_ist_preprocessing · GitHub

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name: scs_segmentation
label: "SCS Segmentation"
summary: "Output of the segmantation methot SCS"
description: "Output of the segmantation methot SCS"
links:
  documentation: "https://github.com/openproblems-bio/task_ist_preprocessing"
  repository: "https://github.com/openproblems-bio/task_ist_preprocessing"
references:
  doi: "10.1038/s41592-023-01939-3"

__merge__: /src/api/comp_method_segmentation.yaml

arguments:
  - name: --env_scs
    type: string
    default: "scs.yaml"


resources:
  - type: bash_script
    path: orchestrator.sh
  - type: python_script
    path: input.py
  - type: file
    path: scs.yaml
    dest: environment.yaml
  - type: python_script
    path: script.py
  - type: python_script
    path: output.py

engines:
  - type: docker
    image: openproblems/base_python:1
    setup:
      - type: python
        pypi: spatialdata
      - type: apt
        packages: ["git", "curl", "libglib2.0-0", "libgl1"]
    __merge__:
      - /src/base/setup_txsim_partial.yaml
  - type: native

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