Trying custom Docker image, exiting properly from stub tests

.gitlab-ci.yml

 ---
 
-image: nextflow/nextflow:22.04.3
+image: trio-whole-exome:v1
 
 test:
   script:

pipeline/var_calling.nf

@@ -37,7 +37,7 @@ process write_bcbio_csv {
 
     script:
     """
-    #!/usr/bin/env python
+    #!/usr/bin/env python3
     import os
 
     target_bed = os.path.realpath('${target_bed}')

tests/Dockerfile

+# Docker image for continuous integration testing in GitLab CI with
+# Docker executor. The image derives from Alma Linux 8.5, and adds
+# NextFlow and basic dependencies (Java, Python, Perl, etc.) but not
+# bioinformatics tools - these should be mocked up in CI with stubs
+
+FROM almalinux:8.6
+
+WORKDIR /opt
+
+RUN dnf install -y java-11-openjdk python3 perl > dnf_install.log 2>&1
+RUN curl -L -o ./nextflow https://github.com/nextflow-io/nextflow/releases/download/v22.04.3/nextflow-22.04.3-all && chmod u+x nextflow
+ENV PATH /opt:$PATH
+ENTRYPOINT /bin/bash

tests/run_stubs.sh

@@ -33,3 +33,4 @@ then
 fi
 
 echo "Tests finished with exit status $test_exit_status"
+exit $test_exit_status