Test step-dependent nextflow configs.

.gitlab-ci.yml

@@ -47,13 +47,23 @@ astrocyte_check:
   script:
   - astrocyte_cli check "$CI_PROJECT_DIR"
   
-nextflow_test:
+nextflow_test_docker:
   stage: test
   script:
   - module load nextflow/20.01.0 
   - module load singularity/3.5.3 
   - cd $CI_PROJECT_DIR/workflow
-  - nextflow  -C $CI_PROJECT_DIR/workflow/configs/biohpc.config  run main.nf -with-trace -with-timeline -resume --verbose
+  - nextflow  -C $CI_PROJECT_DIR/workflow/configs/biohpc_docker.config  run main.nf -with-trace -with-timeline -resume --verbose
+
+
+nextflow_test_singularity:
+  stage: test
+  script:
+  - module load nextflow/20.01.0 
+  - module load singularity/3.5.3 
+  - cd $CI_PROJECT_DIR/workflow
+  - nextflow  -C $CI_PROJECT_DIR/workflow/configs/biohpc_singularity.config  run main.nf -with-trace -with-timeline -resume --verbose
+
 
 # This runs the workflow with test data and does a simple
 # check for the expected output file
@@ -68,6 +78,7 @@ astrocyte_test:
 docker_astrocyte_test:
   stage: test_docker
   script:
+  - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
   - echo "Run astrocyte using dockerhub/docker.io registry pulls"
  
 cache_docker_image:

workflow/configs/biohpc_docker.config

+docker {
+  enabled = true
+}
+
+
+process {
+    executor = 'local'
+}

workflow/configs/biohpc_singularity.config

+singularity {
+  enabled = true
+  runOptions = '--bind /vagrant:/vagrant'
+  cacheDir = "$baseDir/images/singularity"
+}
+
+process {
+    executor = 'local'
+}