Add astrocyte and barnyard tests

.gitlab-ci.yml

@@ -3,6 +3,7 @@
 # chemistries and mouse data.
 
 stages:          # List of stages for jobs, and their order of execution
+  - astrocyte
   - download
   - test
 
@@ -14,27 +15,43 @@ variables:
   GIT_STRATEGY: clone     # Set to avoid expected shallow list error
   GIT_DEPTH: 10           # Set to avoid expected shallow list error
 
-default:
-  tags:
-    - 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
+astrocyte_check:    # Check for astrocyte validity
+  stage: astrocyte
+  tags: 
+    - astrocyte
+  script: 
+    - module load astrocyte/2.0.1
+    - astrocyte_cli check .
 
 download-test-data:       # Download the test data if missing
   stage: download
+  tags:
+    - vm
   script:
     - cd test_data
     - if [ ! -d "Brain_Tumor_3p_LT_fastqs" ]; then ./fetch_Brain_Tumor_3p_LT.sh; fi
+    - if [ ! -d "hgmm_100_fastqs" ]; then ./fetch_hgmm_100.sh; fi
   artifacts:
     paths:
       - test_data/
     expire_in: 2 days
 
-test-cr-count:   # Run cellranger count on the test data
+test-count-human:   # Run cellranger count on the human data
   stage: test
+  tags:
+    - vm
+  before_script:
+     - export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH"
+  script:
+    - nextflow run workflow/main.nf --reference=/data/ref_data/refdata-gex-GRCh38-2020-A --noBam=true
+    - nextflow clean -f -keep-logs
+
+test-count-barnyard:   # Run cellranger count on the barnyard data
+  stage: test
+  tags:
+    - vm
+  before_script:
+     - export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH"
   script:
-    - nextflow run workflow/main.nf --reference=/home/strand_admin/ref/refdata-gex-GRCh38-2020-A --noBam=true # Necessary to run on VM; skip bam generation
-    #- module load nextflow/22.04.5  # Necessary to run on astrocyte
-    #- nextflow run workflow/main.nf
+    - nextflow run workflow/main.nf --fastq=test_data/hgmm_100_fastqs --reference=/data/ref_data/refdata-gex-GRCh38-and-mm10-2020-A --noBam=true
     - nextflow clean -f -keep-logs