Fixing CI testing

.gitlab-ci.yml

@@ -5,10 +5,9 @@ before_script:
   - conda init bash && source ~/.bashrc && echo $CONDA_DEFAULT_ENV
   - conda env create -f environment.yml
   - conda activate mir_pipelines && echo $CONDA_DEFAULT_ENV
-
+  - cd test/
 test:
   script:
-    - cd test
     - bash test_workflow_local.sh
     - bash test_dag.sh
     - bash test_rule_graph.sh

test/test_workflow_local.sh

@@ -24,7 +24,7 @@ snakemake \
 --printshellcmds \
 --snakefile="../snakemake/Snakefile" \
 --use-singularity \
---singularity-args "--no-home --bind ${PWD},${PWD}/../images" \
+--singularity-args "--no-home --bind ${PWD},${PWD}/../../../projects,${PWD}/../images" \
 --cores=4 \
 --rerun-incomplete \
 --configfile config.yaml \