add simple and detailed tests

.gitlab-ci.yml

@@ -3,12 +3,16 @@ 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/0.31.1_Ignite
+  - mkdir test_data/hu.v3s1r500
+  - mkdir test_data/mu.v3s1r500
   - mkdir test_data/hu.v2s1r500
-  - mkdir -p test_data/mu.v2s2r10k
-  - mkdir -p test_data/hu.v3s2r10k
+  - mkdir test_data/hu.v3s2r10k
+  - mkdir test_data/mu.v3s2r10k
+  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s1r500/* test_data/hu.v3s1r500/
+  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v3s1r500/* test_data/mu.v3s1r500/
   - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s1r500/* test_data/hu.v2s1r500/
-  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v2s2r10k/* test_data/mu.v2s2r10k/
   - 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/
 
 stages:
   - astrocyte
@@ -26,10 +30,12 @@ astrocyte_check:
     when:
       - always
 
-run_hu.cr3v2ref3.0.0:
+simple_1:
   stage: simple
+  only: branches
+  except: master
   script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v2s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v2s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'two' --version '3.0.2'
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2'
   - pytest -m count302
   artifacts:
     name: "$CI_JOB_NAME"
@@ -42,13 +48,50 @@ run_hu.cr3v2ref3.0.0:
     when:
       - always
 
-run_mu.cr2v2ref1.2.0:
+simple_2:
+  stage: simple
+  only: branches
+  except: master
+  script:
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1'
+  - pytest -m count301
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - .nextflow.log
+    expire_in: 2 days
+  retry:
+    max: 2
+    when:
+      - always
+
+simple_3:
+  stage: simple
+  only: branches
+  except: master
+  script:
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v2s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v2s1r500/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+  - pytest -m count211
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - .nextflow.log
+    expire_in: 2 days
+  retry:
+    max: 2
+    when:
+      - always
+
+detailed_1:
   stage: detailed
+  only: master
   except:
     - tags
   script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/design.csv" --genome 'mm10-1.2.0' --kitVersion 'auto' --version '2.1.1'
-  - pytest -m count211
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2'
+  - pytest -m count302
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -60,12 +103,13 @@ run_mu.cr2v2ref1.2.0:
     when:
       - always
 
-run_hu.cr3v3ref3.0.0:
+detailed_2:
   stage: detailed
+  only: master
   except:
     - tags
   script:
-  -  nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.2'
   - pytest -m count302
   artifacts:
     name: "$CI_JOB_NAME"

workflow/tests/test_check_design.py

@@ -12,6 +12,10 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 def test_count211_design():
     assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
 
+@pytest.mark.count301
+def test_count301_design():
+    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
+
 @pytest.mark.count302
 def test_count302_design():
     assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))

workflow/tests/test_count.py

@@ -14,6 +14,11 @@ def test_count211_count():
     assert os.path.exists(os.path.join(test_output_path, 'count211', 'sample1_metrics_summary.tsv'))
     assert os.path.exists(os.path.join(test_output_path, 'count211', 'sample1', 'outs'))
 
+@pytest.mark.count301
+def test_count301_count():
+    assert os.path.exists(os.path.join(test_output_path, 'count301', 'sample1_metrics_summary.tsv'))
+    assert os.path.exists(os.path.join(test_output_path, 'count301', 'sample1', 'outs'))
+
 @pytest.mark.count302
 def test_count302_count():
     assert os.path.exists(os.path.join(test_output_path, 'count302', 'sample1_metrics_summary.tsv'))

workflow/tests/test_multiqc.py

@@ -12,6 +12,10 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 def test_count211_multiqc():
     assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))
 
+@pytest.mark.count301
+def test_count301_multiqc():
+    assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))
+
 @pytest.mark.count302
 def test_count302_multiqc():
     assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))

workflow/tests/test_versions.py

@@ -13,6 +13,11 @@ def test_count211_versions():
     assert os.path.exists(os.path.join(test_output_path, 'versions_mqc.yaml'))
     assert os.path.exists(os.path.join(test_output_path, 'references_mqc.yaml'))
 
+@pytest.mark.count301
+def test_count301_versions():
+    assert os.path.exists(os.path.join(test_output_path, 'versions_mqc.yaml'))
+    assert os.path.exists(os.path.join(test_output_path, 'references_mqc.yaml'))
+
 @pytest.mark.count302
 def test_count302_versions():
     assert os.path.exists(os.path.join(test_output_path, 'versions_mqc.yaml'))