.gitlab-ci.yml

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

shallow_run_workflow:
  stage: test
  tags: 
    - stable
  image: 
    name: kaczmarj/apptainer:latest
    entrypoint: [""]
  script:
    ## Downloading apps
    - mkdir appimgs
    #- apptainer build apps/pggb.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangratools/pggb:latest
    - apptainer build appimgs/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

    ## Running workflow
    - mkdir -p data/haplotypes
    - cp example/*.fa.gz data/haplotypes
    - HOME=$(pwd)
    - rm config.yaml && mv example/config_CICD.yaml config.yaml
    - apptainer run --bind $HOME:/root appimgs/snakebox.sif snakemake -c1 --dag > workflow.dot
  artifacts:
    paths:
      - workflow.dot

create_graph:
  stage: deploy
  image: ubuntu:latest
  tags: 
    - stable
  script:
    - apt update -y && apt install dot
    - dot -Tsvg workflow.dot > workflow.svg
  artifacts:
    paths:
      - workflow.svg