Merge CI changes and add more parsing to the CI pipeline

.gitlab-ci.yml

@@ -85,11 +85,16 @@ astrocyte_test:
     - $CI_PROJECT_DIR/workflow/.nextflow.log  
 
 # This runs the workflow, opting to use Docker containers.
+
 docker_astrocyte_test:
   stage: test_docker
+  variables: 
+    config_path : "workflow/configs/"
+    config_filename : "biohpc_docker.config"
   script:
-  - sed -i 's|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27biohpc_docker.config\x27|' astrocyte_pkg.yml
+  - sed -i "s|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27${config_filename}\x27|" astrocyte_pkg.yml
   - echo "Run astrocyte using dockerhub/docker.io registry pulls"
+  - nextflow -C ./${config_path}/${config_filename} config -flat
   - astrocyte_cli run "$CI_PROJECT_DIR" --option=q
   - test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
   tags: