Merge branch 'checks' into 'dev'

fix ci

See merge request epi2melabs/workflow-containers/wf-template!6

.gitlab-ci.yml

@@ -1,4 +1,5 @@
 stages:
+    - pretest
     - test
     - pre-release
     - release-checks 
@@ -22,24 +23,27 @@ variables:
 .check-versions: &check-versions |
     WFVER=$(grep "wfversion = " nextflow.config | awk '{gsub("\"","",$3); print $3}')
     TAGVER=${CI_COMMIT_TAG}
-    if [[ "${PYVER}" != "${WFVER}" ]] then;
-        echo "Mismatching TAG and WORKFLOW versions";
-        exit 1;
-    else;
-        echo "TAG and WORKFLOW versions agree: ${WFVER}";
+    if [[ "${PYVER}" != "${WFVER}" ]]; then
+        echo "Mismatching TAG and WORKFLOW versions:"
+        echo " - TAG:$TAGVER"
+        echo " -  WF:$WFVER"
+        exit 1
+    else
+        echo "TAG and WORKFLOW versions agree: ${WFVER}"
     fi
 
 # Insist a CHANGELOG entry has been made for tags
 .check-changelog: &check-changelog |
     TAGVER=${CI_COMMIT_TAG}
-    MATCHES=$(grep -c "## \[${TAGVER}\]" CHANGELOG.md)
-    if [[ "${MATCHES}" != "1" ]] then;
+    MATCHES=$(grep -c "## \[${TAGVER}\]" CHANGELOG.md || exit 0)
+    if [[ "${MATCHES}" != "1" ]]; then
         echo "Expected one match to '${CI_COMMIT_TAG}' in CHANGELOG, found ${MATCHES}"
         exit 1
-    else;
+    else
         echo "Found CHANGELOG.md entry for tag"
     fi
 
+
 # setup image for pushing to github
 .setup-gh-push: &setup-gh-push |
     apt-get update -qq && apt-get install -y -qq git python3-all-dev git-lfs python3-venv