Git module and container unit tests for seurat

.gitlab-ci.yml

@@ -16,6 +16,7 @@ before_script:
   - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/
   - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v3s2r10k/* test_data/mu.v3s2r10k/
   - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s2r10k/* test_data/hu.v2s2r10k/
+  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/output/* test_data/output/
 
 stages:
   - astrocyte_test
@@ -127,6 +128,31 @@ module_4.0.0_test:
     when:
       - always
 
+module_seurat_test:
+  stage: module_test
+  only:
+    - branches
+  except:
+     refs:
+      - develop
+      - master
+      - tags
+  script:
+    - module load seurat/3.0.0
+    - ln -s test-data/output/* .
+    - seurat-Rscript workflow/scripts/downstream_viz.r --sample sample1 --cellrangerVersion 4.0.0
+    - bash workflow/scripts/versions_seurat.sh > version_seurat.txt
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - version_seurat.txt
+    expire_in: 2 days
+  retry:
+    max: 0
+    when:
+      - always
+
 container_2.1.1_test:
   stage: container_test
   only:
@@ -215,6 +241,30 @@ container_4.0.0_test:
     when:
       - always
 
+container_seurat_test:
+  stage: module_test
+  only:
+    - branches
+  except:
+     refs:
+      - develop
+      - master
+      - tags
+  script:
+    - ln -s test-data/output/* .
+    - singularity run 'docker://bicf/seurat:2.0.0_indev' Rscript workflow/scripts/downstream_viz.r --sample sample1 --cellrangerVersion 4.0.0
+    - singularity run 'docker://bicf/seurat:2.0.0_indev' bash workflow/scripts/versions_seurat.sh > version_seurat.txt
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - version_seurat.txt
+    expire_in: 2 days
+  retry:
+    max: 0
+    when:
+      - always
+
 GRCh38-2020A:
   stage: reference_test
   only: