Add CI updates

.gitlab-ci.yml

@@ -29,6 +29,10 @@ run_hu.cr3v2ref3.0.0:
   stage: simple
   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'
+  - pytest -m design
+  - pytest -m count302
+  - pytest -m versions
+  - pytest -m multiqc
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -46,6 +50,10 @@ run_mu.cr2v2ref1.2.0:
     - tags
   script:
   - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/design.csv" --genome 'mm10-1.2.0' --kitVersion 'auto' --version '2.1.1'
+  - pytest -m design
+  - pytest -m count211
+  - pytest -m versions
+  - pytest -m multiqc
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -62,7 +70,11 @@ run_hu.cr3v3ref3.0.0:
   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 "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
+  - pytest -m design
+  - pytest -m count302
+  - pytest -m versions
+  - pytest -m multiqc
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -72,4 +84,4 @@ run_hu.cr3v3ref3.0.0:
   retry:
     max: 2
     when:
-      - always
\ No newline at end of file
+      - always

workflow/tests/test_check_design.py

+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+		'/../output/misc/checkDesignFile/**/'
+
+@pytest.mark.design
+def test_design():
+    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))

workflow/tests/test_count.py

+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+
+@pytest.mark.count211
+def test_count211():
+    test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                    '/../output/count211/'
+
+@pytest.mark.count301
+def test_count301():
+    test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                    '/../output/count301/'
+
+
+@pytest.mark.count302
+def test_count302():
+    test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                    '/../output/count302/'

workflow/tests/test_multiqc.py

+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                '/../output/multiqc/**/'
+
+@pytest.mark.multiqc
+def test_multiqc():
+    assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))

workflow/tests/test_versions.py

+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                '/../output/misc/versions/**/'
+
+@pytest.mark.versions
+def test_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'))