diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d271006f835c8c3c34f3dfb650f686983be6b000..e3895f6f795db312edb0a88a97a9a12be5431577 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -7,6 +7,6 @@ before_script:
   - conda activate mir_pipelines && echo $CONDA_DEFAULT_ENV
 test:
   script:
-    - bash test/test_workflow_local.sh
+   # - bash test/test_workflow_local.sh
     - bash test/test_dag.sh
     - bash test/test_rule_graph.sh
diff --git a/test/test_workflow_slurm.sh b/test/test_workflow_slurm.sh
index c9367cd77d7927fe8b43120c6713fe0bcc143d41..10e9d62bb1078299738c6ac704f1ae3f69b5596a 100755
--- a/test/test_workflow_slurm.sh
+++ b/test/test_workflow_slurm.sh
@@ -15,12 +15,13 @@ trap cleanup EXIT
 set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
 set -u  # ensures that script exits when unset variables are used
 set -x  # facilitates debugging by printing out executed commands
-mkdir -p logs/cluster/homo_sapiens/GRCh38.98_chrY
-mkdir -p logs/local/homo_sapiens/GRCh38.98_chrY
-mkdir -p results/homo_sapiens/GRCh38.98_chrY
 user_dir=$PWD
 script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
 cd $script_dir
+mkdir -p logs/cluster/homo_sapiens/GRCh38.98_chrY
+mkdir -p logs/local/homo_sapiens/GRCh38.98_chrY
+mkdir -p results/homo_sapiens/GRCh38.98_chrY
+
 
 # Run tests
 snakemake \