.gitlab-ci.yml

# Steps:
# - Getting apps
# - Running the dag
# - Publishing the release with the dag inside

download_apps:
  stage: .pre
  tags: stable
  image:
    name: kaczmarj/apptainer:latest
    entrypoint: [""]
  rules:
    - if: '$CI_COMMIT_BRANCH == "main" && $CI_PIPELINE_SOURCE == "merge_request_event"'
  script:
    - mkdir apps
    #- apptainer build apps/pggb.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangratools/pggb:latest
    - apptainer build apps/snakebox.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangratools/snakebox:latest
    #- apptainer build apps/pytools.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangetools/pytools:latest
    #- apptainer build apps/PanGeTools.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangetools/pangetools:latest

shallow_run_workflow:
  stage: test
  tags: stable
  image: 
    name: kaczmarj/apptainer:latest
    entrypoint: [""]
  rules:
    - if: '$CI_COMMIT_BRANCH == "main" && $CI_PIPELINE_SOURCE == "merge_request_event"'
  script:
    - apptainer run apps/snakebox.sif snakemake -c1 --dag | dot -Tsvg > workflow.svg
  artifacts:
    paths:
      - workflow.svg