Update .gitlab-ci.yml file

.gitlab-ci.yml

@@ -87,9 +87,13 @@ astrocyte_test:
 # 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:
@@ -98,8 +102,9 @@ docker_astrocyte_test:
 cache_docker_image:
   stage: cache_docker
   script:
-  - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+  - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY
   - echo "Pull Docker image from the docker.io registry, re-tag, and push to our GitLab"
+  - docker
   - echo "Need to know what the docker image is ahead of time"
  
 singularity_astrocyte_test: