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Commit f5dd45b3 authored by Alexis Mergez's avatar Alexis Mergez
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CICD changes

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......@@ -12,18 +12,18 @@ shallow_run_workflow:
entrypoint: [""]
script:
## Downloading apps
- mkdir apps
- mkdir appimgs
#- 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 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/* data/haplotypes
- cp example/*.fa.gz data/haplotypes
- HOME=$(pwd)
- ls data/haplotypes
- apptainer run --bind $HOME:/root apps/snakebox.sif snakemake -c1 --dag > workflow.dot
- 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
......
name: '03SC_CICD'
reference: 'R64.fa.gz'
app.path: 'appimgs/'
wfmash.params: '--approx-map'
pggb.params: '-X --skip-viz'
odgi.1Dviz.params: '-x 500 -b'
odgi.pcov.params: '-x 500 -O'
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