fix(ci): specify snakefile in all tests

zavolanlab · Sep 6, 2023 · ead4db9 · ead4db9
1 parent f25a202
commit ead4db9
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Showing 7 changed files with 7 additions and 0 deletions.
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
@@ -26,6 +26,7 @@ cd $script_dir
 
 # Run tests
 snakemake \
+    --snakefile="../../workflow/Snakefile" \
     --profile="../../profiles/local-singularity" \
     --configfile="../input_files/config.yaml" \
     --notemp

diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
@@ -26,6 +26,7 @@ cd $script_dir
 
 # Run tests
 snakemake \
+    --snakefile="../../workflow/Snakefile" \
     --profile="../../profiles/slurm-singularity" \
     --configfile="../input_files/config.yaml" \
     --notemp

diff --git a/tests/test_integration_workflow/test.temp.flag.sh b/tests/test_integration_workflow/test.temp.flag.sh
@@ -26,6 +26,7 @@ cd $script_dir
 
 # Run tests
 snakemake \
+    --snakefile="../../workflow/Snakefile" \
     --profile="../../profiles/local-singularity" \
     --configfile="../input_files/config.yaml"
 

diff --git a/tests/test_integration_workflow_multiple_lanes/test.local.sh b/tests/test_integration_workflow_multiple_lanes/test.local.sh
@@ -26,6 +26,7 @@ cd $script_dir
 
 # Run tests
 snakemake \
+    --snakefile="../../workflow/Snakefile" \
     --profile="../../profiles/local-singularity" \
     --configfile="../input_files/config.mutliple_lanes.yml" \
     --notemp

diff --git a/tests/test_integration_workflow_multiple_lanes/test.slurm.sh b/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
@@ -26,6 +26,7 @@ cd $script_dir
 
 # Run tests
 snakemake \
+    --snakefile="../../workflow/Snakefile" \
     --profile="../../profiles/slurm-singularity" \
     --configfile="../input_files/config.mutliple_lanes.yml" \
     --notemp

diff --git a/tests/test_integration_workflow_with_conda/test.local.sh b/tests/test_integration_workflow_with_conda/test.local.sh
@@ -26,6 +26,7 @@ cd $script_dir
 
 # Run tests
 snakemake \
+    --snakefile="../../workflow/Snakefile" \
     --profile="../../profiles/local-conda" \
     --configfile="../input_files/config.yaml" \
     --notemp

diff --git a/tests/test_integration_workflow_with_conda/test.slurm.sh b/tests/test_integration_workflow_with_conda/test.slurm.sh
@@ -26,6 +26,7 @@ cd $script_dir
 
 # Run tests
 snakemake \
+    --snakefile="../../workflow/Snakefile" \
     --profile="../../profiles/slurm-conda" \
     --configfile="../input_files/config.yaml" \
     --notemp