Update Giblab CI

.gitlab-ci.yml

@@ -7,6 +7,8 @@
 stages:
     - check
     - test
+    - run
+    - viz
 
 variables:
     GIT_STRATEGY: clone
@@ -49,6 +51,19 @@ astrocyte_test:
   extends: .astrocyte
   stage: test
   script:
+  - astrocyte_cli test "$CI_PROJECT_DIR"
+  - test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.cleanlines.wordcount"
+  artifacts:
+    paths:
+    - $CI_PROJECT_DIR/workflow/.nextflow.log  
+
+# This runs the workflow with test data and does a simple check for the expected output file.
+#  This assumes that the 'default' config uses local processing, not containers.
+astrocyte_run:
+  extends: .astrocyte
+  stage: run
+  script:
+  - rm -f "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.cleanlines.wordcount"
   - astrocyte_cli run "$CI_PROJECT_DIR" --option=q
   - test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.cleanlines.wordcount"
   artifacts:
@@ -60,7 +75,7 @@ astrocyte_test:
 # and start the vizapp running.
 astrocyte_viz:
   extends: .astrocyte
-  stage: test
+  stage: viz
   script:
   - astrocyte_cli viz-prepare "$CI_PROJECT_DIR"
   - 'timeout 10 astrocyte_cli viz "$CI_PROJECT_DIR" &'