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# Steps:
# - Getting apps
# - Running the dag
# - Publishing the release with the dag inside
name: kaczmarj/apptainer:latest
entrypoint: [""]
script:
#- 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
- rm config.yaml && mv example/config_CICD.yaml config.yaml
- apptainer run --bind $HOME:/root appimgs/snakebox.sif snakemake -c1 --dag > workflow.dot
create_graph:
stage: deploy
image: ubuntu:latest
- apt update -y && apt install dot
- dot -Tsvg workflow.dot > workflow.svg
artifacts:
paths:
- workflow.svg