CICD changes

.gitlab-ci.yml

@@ -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

example/config_CICD.yaml

+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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