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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 pull appimgs/snakebox.sif oras://registry.forgemia.inra.fr/alexis.mergez/pan1capps/pan1cbox: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 $HOME:/root appimgs/snakebox.sif snakemake -c1 --dag > workflow.dot
create_graph:
stage: deploy
image: ubuntu:latest
# deep_run_workflow:
# stage: test
# image:
# name: kaczmarj/apptainer:latest
# entrypoint: [""]
# tags:
# - custom
# script:
# ## Downloading apps
# - mkdir appimgs
# - apptainer build appimgs/PanGeTools.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangetools/pangetools:latest
# - apptainer build appimgs/pan1c-env.sif oras://registry.forgemia.inra.fr/alexis.mergez/pan1capps/pan1cenv:latest
# - apptainer build appimgs/pggb.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangratools/pggb:latest
# - apptainer build appimgs/pan1c-box.sif oras://registry.forgemia.inra.fr/alexis.mergez/pan1capps/pan1cbox:latest
# ## Running workflow
# - mkdir -p data/haplotypes
# - cp example/*.fa.gz data/haplotypes
# - HOME=$(pwd)
# - rm config.yaml && mv example/config_CICD.yaml config.yaml
# - apptainer run --bind $HOME:/root appimgs/pan1c-box.sif snakemake -c 4
# artifacts:
# paths:
# - output/pan1c.pggb.03SC_CICD.gfa
# - output/pan1c.pggb.03SC_CICD.workflow.stats.tsv
# allow_failure: true