Merge branch 'verbose_tests' into 'master'

run tests in verbose mode

Closes #68

See merge request zavolan_group/pipelines/rnaseqpipeline!26

.gitlab-ci.yml

@@ -10,8 +10,8 @@ test:
     # add code quality tests here
     # add unit tests here
     # add script tests here
-    - bash tests/test_scripts_table_to_snakemake/test.sh
-    - bash tests/test_scripts_labkey_to_snakemake/test.sh
+    - bash tests/test_scripts_labkey_to_snakemake_table/test.sh
+    - bash tests/test_scripts_labkey_to_snakemake_api/test.sh
     # add integration tests here
     - bash tests/test_create_dag_image/test.sh
     - bash tests/test_create_rule_graph/test.sh

tests/test_create_dag_image/test.sh

 #!/bin/bash
 
 # Tear down test environment
-trap 'rm -rf .snakemake && cd $user_dir' EXIT  # quotes command is exected after script exits, regardless of exit status
+cleanup () {
+    rc=$?
+    rm -rf .snakemake
+    cd $user_dir
+    echo "Exit status: $rc"
+}
+trap cleanup EXIT
 
 # Set up test environment
 set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
@@ -18,5 +24,6 @@ snakemake \
     --dag \
     --printshellcmds \
     --dryrun \
+    --verbose \
     | dot -Tsvg > "../../images/dag_test_workflow.svg"
 

tests/test_create_rule_graph/test.sh

 #!/bin/bash
 
 # Tear down test environment
-trap 'rm -rf .snakemake && cd $user_dir' EXIT  # quotes command is exected after script exits, regardless of exit status
+cleanup () {
+    rc=$?
+    rm -rf .snakemake
+    cd $user_dir
+    echo "Exit status: $rc"
+}
+trap cleanup EXIT
 
 # Set up test environment
 set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
@@ -18,5 +24,6 @@ snakemake \
     --rulegraph \
     --printshellcmds \
     --dryrun \
+    --verbose \
     | dot -Tsvg > "../../images/rule_graph.svg"
 

tests/test_integration_workflow/test.local.sh

 #!/bin/bash
 
 # Tear down test environment
-trap 'rm -rf logs/ results/ .snakemake/ .java/ local_log/ && cd $user_dir' EXIT  # quoted command is exected after script exits, regardless of exit status
+cleanup () {
+    rc=$?
+    rm -rf .java/
+    rm -rf .snakemake/
+    rm -rf local_log/
+    rm -rf logs/
+    rm -rf results/
+    cd $user_dir
+    echo "Exit status: $rc"
+}
+trap cleanup EXIT
 
 # Set up test environment
 set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
@@ -20,7 +30,8 @@ snakemake \
     --printshellcmds \
     --rerun-incomplete \
     --use-singularity \
-    --singularity-args="--bind ${PWD}/../input_files"
+    --singularity-args="--bind ${PWD}/../input_files" \
+    --verbose
 
 # Check md5 sum of some output files
 find results/ -type f -name \*\.gz -exec gunzip '{}' \;

tests/test_integration_workflow/test.slurm.sh

 #!/bin/bash
 
 # Tear down test environment
-trap 'rm -rf logs/ results/ .snakemake/ .java/ local_log/ && cd $user_dir' EXIT  # quoted command is exected after script exits, regardless of exit status
+cleanup () {
+    rc=$?
+    rm -rf .java/
+    rm -rf .snakemake/
+    rm -rf local_log/
+    rm -rf logs/
+    rm -rf results/
+    cd $user_dir
+    echo "Exit status: $rc"
+}
+trap cleanup EXIT
 
 # Set up test environment
 set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
@@ -23,7 +33,8 @@ snakemake \
     --printshellcmds \
     --rerun-incomplete \
     --use-singularity \
-    --singularity-args="--bind ${PWD}/../input_files"
+    --singularity-args="--bind ${PWD}/../input_files" \
+    --verbose
 
 # Check md5 sum of some output files
 find results/ -type f -name \*\.gz -exec gunzip '{}' \;

tests/test_scripts_labkey_to_snakemake/test.sh → tests/test_scripts_labkey_to_snakemake_api/test.sh

@@ -4,7 +4,17 @@
 # 'LABKEY_PASS' to be set with the appropriate values
 
 # Tear down test environment
-trap 'rm -rf ${HOME}/.netrc .snakemake config.yaml samples.tsv input_table.tsv && cd $user_dir' EXIT  # quotes command is exected after script exits, regardless of exit status
+cleanup () {
+    rc=$?
+    rm -rf ${HOME}/.netrc
+    rm -rf .snakemake/
+    rm -rf config.yaml
+    rm -rf input_table.tsv
+    rm -rf samples.tsv
+    cd $user_dir
+    echo "Exit status: $rc"
+}
+trap cleanup EXIT
 
 # Set up test environment
 set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
@@ -36,6 +46,7 @@ snakemake \
     --snakefile="../../Snakefile" \
     --configfile="config.yaml" \
     --dryrun \
+    --verbose
 
 md5sum --check "expected_output.md5"
 # MD5 sums obtained with command:

tests/test_scripts_table_to_snakemake/test.sh → tests/test_scripts_labkey_to_snakemake_table/test.sh

 #!/bin/bash
 
 # Tear down test environment
-trap 'rm -rf .snakemake config.yaml samples.tsv && cd $user_dir' EXIT  # quotes command is exected after script exits, regardless of exit status
+cleanup () {
+    rc=$?
+    rm -rf .snakemake/
+    rm -rf config.yaml
+    rm -rf samples.tsv
+    cd $user_dir
+    echo "Exit status: $rc"
+}
+trap cleanup EXIT
 
 # Set up test environment
 set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
@@ -25,6 +33,7 @@ snakemake \
     --snakefile="../../Snakefile" \
     --configfile="config.yaml" \
     --dryrun \
+    --verbose
 
 md5sum --check "expected_output.md5"
 # MD5 sums obtained with command: