Merge branch '25-AddPytestCI' into 'develop'

Resolve "Add pytest to CI"

Closes #25

See merge request !40

.gitlab-ci.yml

 before_script:
   - module load astrocyte
   - 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 -p test_data/simple1
   - mkdir -p test_data/simple2
@@ -28,6 +29,7 @@ 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 simple1
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -43,6 +45,7 @@ simple_2FC:
   stage: simple
   script:
     - nextflow run workflow/main.nf --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv"
+    - pytest -m simple2
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -52,4 +55,4 @@ simple_2FC:
   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/run/'
+
+@pytest.mark.simple1
+def test_simple1_design():
+    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
+
+@pytest.mark.simple2
+def test_simple2_design():
+    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))    

workflow/tests/test_fastqc.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/fastqc/run/'
+
+@pytest.mark.simple1
+def test_simple1_fastqc():
+    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0'))
+
+@pytest.mark.simple2
+def test_simple2_fastqc():
+    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-1'))
+    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-2'))

workflow/tests/test_mkfastq.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/mkfastq/'
+
+@pytest.mark.simple1
+def test_simple1_mkfastq():
+    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0', 'outs'))
+
+@pytest.mark.simple2
+def test_simple2_mkfastq():
+    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-1', 'outs'))
+    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-2', 'outs'))

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/run/'
+
+@pytest.mark.simple1
+def test_simple1_multiqc():
+    assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))
+
+@pytest.mark.simple2
+def test_simple2_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__)) + \
+                '/../output/untarBCL/'
+
+@pytest.mark.simple1
+def test_simple1_untarBCL():
+    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0', 'RTAComplete.txt'))
+
+@pytest.mark.simple2
+def test_simple2_untarBCL():
+    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-1', 'RTAComplete.txt'))
+    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-2', '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__)) + \
+                '/../output/misc/versions/run/'
+
+@pytest.mark.simple1
+def test_simple1_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.simple2
+def test_simple2_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'))