type: ArcWorkspaceProfile
id: arc.isa.yml.scaffold
version: "1.0"
description: ISA Dataset-YAML decoration scaffold

rules:
  - id: investigation
    codec: dataset.yml
    target: root
    path: isa.investigation.yml

  - id: study
    codec: dataset.yml
    target:
      additionalType: Study
    path: "studies/{dataset.identifier}/isa.study.yml"
    files:
      - id: resources-placeholder
        path: resources/.gitkeep
        create: empty
      - id: protocols-placeholder
        path: protocols/.gitkeep
        create: empty

  - id: assay
    codec: dataset.yml
    target:
      additionalType: Assay
    path: "assays/{dataset.identifier}/isa.assay.yml"
    files:
      - id: dataset-placeholder
        path: dataset/.gitkeep
        create: empty
      - id: protocols-placeholder
        path: protocols/.gitkeep
        create: empty

  - id: workflow
    codec: dataset.yml
    target:
      additionalType: Workflow
    path: "workflows/{dataset.identifier}/isa.workflow.yml"
    files:
      - id: protocols-placeholder
        path: protocols/.gitkeep
        create: empty

  - id: run
    codec: dataset.yml
    target:
      additionalType: Run
    path: "runs/{dataset.identifier}/isa.run.yml"
    files:
      - id: dataset-placeholder
        path: dataset/.gitkeep
        create: empty
      - id: protocols-placeholder
        path: protocols/.gitkeep
        create: empty