Update CI for 4.0.0/2020-A

.gitlab-ci.yml

@@ -105,6 +105,30 @@ astrocyte_cli:
     when:
       - always
 
+GRCh38-2020A:
+  stage: reference_test
+  only:
+    refs:
+      - develop
+      - master
+  except:
+    - tags
+  script:
+  - nextflow run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-2020-A' --kitVersion '3GEXv3' --version '4.0.0' --ci true
+  - pytest -m count400
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - .nextflow.log
+      - workflow/output/count400/sample1/outs/web_summary.html
+      - workflow/output/multiqc/run/multiqc_report.html
+    expire_in: 2 days
+  retry:
+    max: 0
+    when:
+      - always
+
 GRCh38-3.0.0:
   stage: reference_test
   only:
@@ -129,6 +153,30 @@ GRCh38-3.0.0:
     when:
       - always
 
+mm10-2020A:
+  stage: reference_test
+  only:
+    refs:
+      - develop
+      - master
+  except:
+    - tags
+  script:
+  - nextflow run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-2020-A' --kitVersion '3GEXv3' --version '4.0.0' --ci true
+  - pytest -m count400
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - .nextflow.log
+      - workflow/output/count400/sample1/outs/web_summary.html
+      - workflow/output/multiqc/run/multiqc_report.html
+    expire_in: 2 days
+  retry:
+    max: 0
+    when:
+      - always
+
 mm10-3.0.0:
   stage: reference_test
   only:
@@ -160,15 +208,15 @@ mm10-3.0.0:
       - master
       - tags
   script:
-  - nextflow run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.1.0' --ci true
-  - pytest -m count310
+  - nextflow run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-2020A' --kitVersion 'auto' --version '4.0.0' --ci true
+  - pytest -m count400
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
     paths:
       - .nextflow.log
-      - workflow/output/count310/sample1/outs/web_summary.html
-      - workflow/output/count310/sample2/outs/web_summary.html
+      - workflow/output/count400/sample1/outs/web_summary.html
+      - workflow/output/count400/sample2/outs/web_summary.html
       - workflow/output/multiqc/run/multiqc_report.html
     expire_in: 2 days
   retry:

workflow/tests/test_count.py

@@ -33,4 +33,9 @@ def test_count302_count():
 @pytest.mark.count310
 def test_count310_count():
     assert os.path.exists(os.path.join(test_output_path, 'count310', 'sample1_metrics_summary.tsv'))
-    assert os.path.exists(os.path.join(test_output_path, 'count310', 'sample1', 'outs'))
\ No newline at end of file
+    assert os.path.exists(os.path.join(test_output_path, 'count310', 'sample1', 'outs'))
+
+@pytest.mark.count400
+def test_count310_count():
+    assert os.path.exists(os.path.join(test_output_path, 'count400', 'sample1_metrics_summary.tsv'))
+    assert os.path.exists(os.path.join(test_output_path, 'count400', 'sample1', 'outs'))