Add integration test

.gitlab-ci.yml

@@ -16,6 +16,7 @@ variables:
 stages:
   - sanity
   - dry-run
+  - integration
 
 test-sanity:
   <<: *before_script_anchor
@@ -34,3 +35,12 @@ test-dry-run:
   tags:
     - docker
   stage: dry-run
+
+test-integration:
+  <<: *slurm_before_script_anchor
+  script:
+    - pytest --keep-workflow-wd-on-fail --basetemp ${BASETEMP} --tag integration
+  image: lumc/singularity-snakemake:3.5.2-5.15.0
+  tags:
+    - slurm
+  stage: integration