Add split unit tests for modules and containers

.gitlab-ci.yml

@@ -3,7 +3,7 @@ before_script:
   - module load python/3.6.1-2-anaconda
   - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
   - module load nextflow/20.01.0
-  - module load singularity/3.0.2
+  - module load singularity/3.5.3
   - mkdir -p test_data/hu.v2s1r500
   - mkdir -p test_data/hu.v3s1r500
   - mkdir -p test_data/mu.v3s1r500
@@ -19,6 +19,7 @@ before_script:
 
 stages:
   - astrocyte_test
+  - module_test
   - container_test
   - reference_test
   - multiSample_test
@@ -34,8 +35,8 @@ astrocyte_cli:
     when:
       - always
 
-2.1.1_test:
-  stage: container_test
+module_2.1.1_test:
+  stage: module_test
   only:
     - branches
   except:
@@ -57,8 +58,8 @@ astrocyte_cli:
     when:
       - always
 
-3.0.2_test:
-  stage: container_test
+module_3.0.2_test:
+  stage: module_test
   only:
     - branches
   except:
@@ -80,8 +81,8 @@ astrocyte_cli:
     when:
       - always
 
-3.1.0_test:
-  stage: container_test
+module_3.1.0_test:
+  stage: module_test
   only:
     - branches
   except:
@@ -105,8 +106,8 @@ astrocyte_cli:
     when:
       - always
 
-4.0.0_test:
-  stage: container_test
+module_4.0.0_test:
+  stage: module_test
   only:
     - branches
   except:
@@ -130,6 +131,98 @@ astrocyte_cli:
     when:
       - always
 
+container_2.1.1_test:
+  stage: container_test
+  only:
+    - branches
+  except:
+    refs:
+      - develop
+      - master
+      - tags
+  script:
+    - singularity run 'docker://bicf/cellranger2.1.1:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - test/outs/web_summary.html
+    expire_in: 2 days
+  retry:
+    max: 0
+    when:
+      - always
+
+container_3.0.2_test:
+  stage: container_test
+  only:
+    - branches
+  except:
+    refs:
+      - develop
+      - master
+      - tags
+  script:
+    - singularity run 'docker://bicf/cellranger3.0.2:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - test/outs/web_summary.html
+    expire_in: 2 days
+  retry:
+    max: 0
+    when:
+      - always
+
+container_3.1.0_test:
+  stage: container_test
+  only:
+    - branches
+  except:
+     refs:
+      - develop
+      - master
+      - tags
+  script:
+    - singularity run 'docker://bicf/cellranger3.1.0:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - develop
+      - master
+      - test/outs/web_summary.html
+    expire_in: 2 days
+  retry:
+    max: 0
+    when:
+      - always
+
+container_4.0.0_test:
+  stage: container_test
+  only:
+    - branches
+  except:
+     refs:
+      - develop
+      - master
+      - tags
+  script:
+    - singularity run 'docker://bicf/cellranger4.0.0:2.0.0_indev' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-gex-GRCh38-2020-A --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - develop
+      - master
+      - test/outs/web_summary.html
+    expire_in: 2 days
+  retry:
+    max: 0
+    when:
+      - always
+
 GRCh38-2020A:
   stage: reference_test
   only: