Update .gitlab-ci.yml

.gitlab-ci.yml

@@ -22,7 +22,7 @@ shallow_run_workflow:
     - mkdir data
     - ln -s example data/haplotypes
     - pwd && ls
-    - apptainer run apps/snakebox.sif snakemake -c1 --dag > workflow.dot
+    - apptainer run apps/snakebox.sif 'pwd && ls && snakemake -c1 --dag > workflow.dot'
   artifacts:
     paths:
       - workflow.dot