Add custom pytest-workflow test to ensure versions.yml is valid

.gitignore

@@ -7,3 +7,6 @@ output/
 *.code-workspace
 .screenrc
 .*.sw?
+__pycache__
+*.pyo
+*.pyc

modules/fastqc/functions.nf

@@ -44,7 +44,9 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.equals('versions.yml')) {
+    // TODO better way to detect that we are in a test and want to emit `versions.yml`
+    // or a least use a dedicated, unique environment variable.
+    if (!args.filename.equals('versions.yml') || System.getenv("PROFILE")) {
         def ioptions  = initOptions(args.options)
         def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
         if (ioptions.publish_by_meta) {

tests/__init__.py

@@ -0,0 +1,2 @@
+# Makes the tests directory a python module
+# (required to obtain resources from this folder from within Python)

tests/test_versions_yml.py

@@ -0,0 +1,23 @@
+from pathlib import Path
+import pytest
+import yaml
+
+
+def _get_workflow_names():
+    here = Path(__file__).parent.resolve()
+    pytest_workflow_files = here.glob("**/test.yml")
+    for f in pytest_workflow_files:
+        test_config = yaml.safe_load(f.read_text())
+        for workflow in test_config:
+            yield workflow["name"]
+
+
+@pytest.mark.workflow(*_get_workflow_names())
+def test_ensure_valid_version_yml(workflow_dir):
+    workflow_dir = Path(workflow_dir)
+    software_name = workflow_dir.name.split("_")[0].lower()
+    versions_yml = Path(
+        workflow_dir, f"output/{software_name}/versions.yml"
+    ).read_text()
+    assert "END_VERSIONS" not in versions_yml
+    yaml.safe_load(versions_yml)