repo follows recommended structure

.gitlab-ci.yml

@@ -13,6 +13,6 @@ test:
     - bash tests/test_scripts_labkey_to_snakemake/test.sh
     # add integration tests here
     - bash tests/test_create_dag_image/test.sh
-    - bash tests/test_rule_graph/test.sh
+    - bash tests/test_create_rule_graph/test.sh
     - bash tests/test_integration_workflow/test.local.sh
 

snakemake/Snakefile → Snakefile

@@ -18,8 +18,8 @@ localrules: finish
 # Execution dependend on sequencing mode
 ##################################################################################
 
-include: 'paired_end.snakefile.smk'
-include: 'single_end.snakefile.smk'
+include: os.path.join('workflow', 'rules', 'paired_end.snakefile.smk')
+include: os.path.join('workflow', 'rules', 'single_end.snakefile.smk')
 
 #################################################################################
 ### Final rule

tests/test_create_dag_image/test.sh

 #!/bin/bash
 
 # Tear down test environment
-trap 'cd $user_dir' EXIT  # quotes command is exected after script exits, regardless of exit status
+trap 'rm -rf .snakemake && cd $user_dir' EXIT  # quotes command is exected after script exits, regardless of exit status
 
 # Set up test environment
 set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
@@ -13,7 +13,7 @@ cd $script_dir
 
 # Run tests
 snakemake \
-    --snakefile="../../snakemake/Snakefile" \
+    --snakefile="../../Snakefile" \
     --configfile="config.yaml" \
     --dag \
     --printshellcmds \

tests/test_rule_graph/test.sh → tests/test_create_rule_graph/test.sh

 #!/bin/bash
 
 # Tear down test environment
-trap 'cd $user_dir' EXIT  # quotes command is exected after script exits, regardless of exit status
+trap 'rm -rf .snakemake && cd $user_dir' EXIT  # quotes command is exected after script exits, regardless of exit status
 
 # Set up test environment
 set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
@@ -13,7 +13,7 @@ cd $script_dir
 
 # Run tests
 snakemake \
-    --snakefile="../../snakemake/Snakefile" \
+    --snakefile="../../Snakefile" \
     --configfile="config.yaml" \
     --rulegraph \
     --printshellcmds \

tests/test_integration_workflow/test.local.sh

@@ -14,7 +14,7 @@ mkdir -p logs/local_log
 
 # Run tests
 snakemake \
-    --snakefile="../../snakemake/Snakefile" \
+    --snakefile="../../Snakefile" \
     --configfile="config.yaml" \
     --cores=4 \
     --printshellcmds \

tests/test_integration_workflow/test.slurm.sh

@@ -15,7 +15,7 @@ mkdir -p logs/local_log
 
 # Run tests
 snakemake \
-    --snakefile="../../snakemake/Snakefile" \
+    --snakefile="../../Snakefile" \
     --configfile="config.yaml" \
     --cluster-config="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" \

tests/test_scripts_labkey_to_snakemake/test.sh

 #!/bin/bash
 
 # Tear down test environment
-trap 'rm config.yaml samples.tsv && cd $user_dir' EXIT  # quotes command is exected after script exits, regardless of exit status
+trap 'rm -rf config.yaml samples.tsv .snakemake && cd $user_dir' EXIT  # quotes command is exected after script exits, regardless of exit status
 # 
 # Set up test environment
 set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
@@ -25,7 +25,7 @@ python "../../scripts/labkey_to_snakemake.py" \
 
 
 snakemake \
-    --snakefile="../../snakemake/Snakefile" \
+    --snakefile="../../Snakefile" \
     --configfile="config.yaml" \
     --dryrun \
     # --rulegraph \