diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
index c6c84103ee873c4546487b6b9ed7af58be2f6112..6c40abba6ba761899bd224c3a87a8f02ebf0df3c 100755
--- a/tests/test_integration_workflow/test.slurm.sh
+++ b/tests/test_integration_workflow/test.slurm.sh
@@ -26,7 +26,7 @@ cd $script_dir
 
 # Run tests
 snakemake \
-    --snakefile="../../Snakefile" \
+    --snakefile="../../workflow/Snakefile" \
     --configfile="../input_files/config.yaml" \
     --cluster-config="../input_files/cluster.json" \
     --cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
@@ -41,7 +41,7 @@ snakemake \
 
 # Create a Snakemake report after the workflow execution
 snakemake \
-    --snakefile="../../Snakefile" \
+    --snakefile="../../workflow/Snakefile" \
     --configfile="../input_files/config.yaml" \
     --report="snakemake_report.html"
 
diff --git a/tests/test_integration_workflow_multiple_lanes/test.slurm.sh b/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
index 74ba028f9ef4ac85543657916adbfbe45de25c9e..10a2752b9531e36c2d23d07ba1950b2a4607f066 100755
--- a/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
+++ b/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
@@ -26,7 +26,7 @@ cd $script_dir
 
 # Run tests
 snakemake \
-    --snakefile="../../Snakefile" \
+    --snakefile="../../workflow/Snakefile" \
     --configfile="../input_files/config.mutliple_lanes.yml" \
     --cluster-config="../input_files/cluster.json" \
     --cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
@@ -41,7 +41,7 @@ snakemake \
 
 # Create a Snakemake report after the workflow execution
 snakemake \
-    --snakefile="../../Snakefile" \
+    --snakefile="../../workflow/Snakefile" \
     --configfile="../input_files/config.mutliple_lanes.yml" \
     --report="snakemake_report.html"
 
diff --git a/tests/test_integration_workflow_with_conda/test.slurm.sh b/tests/test_integration_workflow_with_conda/test.slurm.sh
index e4a7009040415e42ec4e991b28be31776f2c31bc..873f17bafcc6bdf9f7a9718793fea3d97ef8eed4 100755
--- a/tests/test_integration_workflow_with_conda/test.slurm.sh
+++ b/tests/test_integration_workflow_with_conda/test.slurm.sh
@@ -3,14 +3,14 @@
 # Tear down test environment
 cleanup () {
     rc=$?
-    # rm -rf .cache/
-    # rm -rf .config/
-    # rm -rf .fontconfig/
-    # rm -rf .java/
-    # rm -rf .snakemake/
-    # rm -rf logs/
-    # rm -rf results/
-    # rm -rf snakemake_report.html
+    rm -rf .cache/
+    rm -rf .config/
+    rm -rf .fontconfig/
+    rm -rf .java/
+    rm -rf .snakemake/
+    rm -rf logs/
+    rm -rf results/
+    rm -rf snakemake_report.html
     cd $user_dir
     echo "Exit status: $rc"
 }
@@ -26,7 +26,7 @@ cd $script_dir
 
 # Run tests
 snakemake \
-    --snakefile="../../Snakefile" \
+    --snakefile="../../workflow/Snakefile" \
     --configfile="../input_files/config.yaml" \
     --cluster-config="../input_files/cluster.json" \
     --cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
@@ -40,7 +40,7 @@ snakemake \
 
 # Create a Snakemake report after the workflow execution
 snakemake \
-    --snakefile="../../Snakefile" \
+    --snakefile="../../workflow/Snakefile" \
     --configfile="../input_files/config.yaml" \
     --report="snakemake_report.html"