Add tests for all sections of pipeline

.gitlab-ci.yml

@@ -28,7 +28,12 @@ simple_1FC:
     - tags
   script:
     - nextflow run workflow/main.nf --bcl "test_data/simple1/*.tar.gz" --designFile "test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv"
+    - pytest -m design 
+    - pytest -m untarBCL
+    - pytest -m mkfastq
     - pytest -m fastqc
+    - pytest -m versions
+    - pytest -m multiqc
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -44,7 +49,12 @@ simple_2FC:
   stage: simple
   script:
     - nextflow run workflow/main.nf --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv"
+    - pytest -m design
+    - pytest -m untarBCL
+    - pytest -m mkfastq
     - pytest -m fastqc
+    - pytest -m versions
+    - pytest -m multiqc
   artifacts:
     name: "$CI_JOB_NAME"
     when: 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__)) + \
+                '/../../test/misc/checkDesignFile/**/'
+
+@pytest.mark.design
+def test_design():
+    assert os.path.exists(os.path.join(test_output_path, design.checked.csv))

workflow/tests/test_fastqc.py

@@ -4,13 +4,12 @@ import pytest
 import pandas as pd
 from io import StringIO
 import os
-import glob
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-		'/../../test/mkfastq/**/outs/fastq_path/**/**/'
+                '/../../test/misc/fastqc/**/**/'
 
 @pytest.mark.fastqc
-def test_fastqc_output():
-    fastqcs = glob.glob('/../../test/mkfastq/*/outs/fastq_path/*/*/*.fastq.gz', recursive=True)
+def test_fastqc():
+    fastqcs = glob.glob('/../../test/misc/fastqc/*/*/*fastqc.zip', recursive=True)
     for f in fastqcs:
         assert os.path.exists(os.path.join(test_output_path, f))

workflow/tests/test_mkfastq.py

+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+import glob
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+		'/../../test/mkfastq/**/outs/fastq_path/**/**/'
+
+@pytest.mark.mkfastq
+def test_mkfastq():
+    fastqcs = glob.glob('/../../test/mkfastq/*/outs/fastq_path/*/*/*.fastq.gz', recursive=True)
+    for f in fastqcs:
+        assert os.path.exists(os.path.join(test_output_path, f))

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__)) + \
+                '/../../test/multiqc/**/'
+
+@pytest.mark.multiqc
+def test_multiqc():
+    assert os.path.exists(os.path.join(test_output_path, multiqc_report.html))

workflow/tests/test_untarBCL.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__)) + \
+                '/../../test/untarBCL/**/'
+
+@pytest.mark.untarBCL
+def test_untarBCL():
+    assert os.path.exists(os.path.join(test_output_path, RTAComplete.txt))

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__)) + \
+                '/../../test/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))