Skip ref download and clean nf work

.gitlab-ci.yml

@@ -16,30 +16,25 @@ variables:
 
 default:
   tags:
-    #- vm  # Pass jobs to the VM runner
-    - astrocyte  # Pass jobs to the astrocyte runner
+    - vm  # Pass jobs to the VM runner
+    #- astrocyte  # Pass jobs to the astrocyte runner
   before_script:
-    # - export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH"  # Necessary to run on VM
+     - export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH"  # Necessary to run on VM
 
 download-test-data:       # Download the test data if missing
   stage: download
-  rules: 
-    - exists:
-      - "test_data/Brain_Tumor_3p_LT_fastqs"
-      when: never
-    - when: always
   script:
     - cd test_data
-    - ./fetch_Brain_Tumor_3p_LT.sh
-    - echo "Download complete."
+    - if [ ! -d "test_data/Brain_Tumor_3p_LT_fastqs" ]; then ./fetch_Brain_Tumor_3p_LT.sh; fi
   artifacts:
     paths:
       - test_data/
     expire_in: 2 days
 
-test-cr-count:   # Test cellranger count on the test data
+test-cr-count:   # Run cellranger count on the test data
   stage: test
   script:
-    #- nextflow run workflow/main.nf --reference=/home/strand_admin/ref/refdata-gex-GRCh38-2020-A  # Necessary to run on VM
-    - module load nextflow/22.04.5
-    - nextflow run workflow/main.nf
\ No newline at end of file
+    - nextflow run workflow/main.nf --reference=/home/strand_admin/ref/refdata-gex-GRCh38-2020-A  # Necessary to run on VM
+    #- module load nextflow/22.04.5  # Necessary to run on astrocyte
+    - nextflow run workflow/main.nf
+    - nextflow clean -keep-logs