diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 3040c3d333f88ef61dd97181445ab7efb1ffc949..f0a8dce734065c30436e9cd606e652d3eae157af 100644 --- a/.gitlab-ci.yml +++ b/.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 diff --git a/test/test_workflow_local.sh b/test/test_workflow_local.sh index f267712c7c2bed0fd29bf91177f2d9e86c048eb0..7c234ebf7e6744c9875333de7feffd0138482e4d 100755 --- a/test/test_workflow_local.sh +++ b/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 \