restructre pytests

.gitlab-ci.yml

@@ -29,12 +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 design
-    - pytest -m untarBCL
-    - pytest -m mkfastq
-    - pytest -m fastqc
-    - pytest -m versions
-    - pytest -m multiqc
+    - pytest -m simple1
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -50,12 +45,7 @@ simple_2FC:
   stage: simple
   script:
     - nextflow run workflow/main.nf --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv"
-    - pytest -m design
-    - pytest -m untarBCL
-    - pytest -m mkfastq
-    - pytest -m fastqc
-    - pytest -m versions
-    - pytest -m multiqc
+    - pytest -m simple2
   artifacts:
     name: "$CI_JOB_NAME"
     when: always

workflow/tests/test_check_design.py

@@ -8,7 +8,10 @@ import os
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/misc/checkDesignFile/run/'
 
-@pytest.mark.design
-def test_design():
-    design_file = os.path.join(test_output_path, 'design.checked.csv')
-    assert os.path.exists(design_file)
+@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

@@ -6,8 +6,13 @@ from io import StringIO
 import os
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-                '/../output/misc/fastqc/run/cellranger-tiny-bcl-1_2_0/'
+                '/../output/misc/fastqc/run/'
 
-@pytest.mark.fastqc
-def test_fastqc():
-    assert os.path.exists(test_output_path)
+@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

@@ -4,11 +4,15 @@ import pytest
 import pandas as pd
 from io import StringIO
 import os
-import glob
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-		'/../output/mkfastq/cellranger-tiny-bcl-1_2_0/outs/'
+		'/../output/mkfastq/'
 
-@pytest.mark.mkfastq
-def test_mkfastq():
-    assert os.path.exists(test_output_path)
+@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

@@ -8,6 +8,10 @@ import os
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/multiqc/run/'
 
-@pytest.mark.multiqc
-def test_multiqc():
+@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

@@ -6,8 +6,13 @@ from io import StringIO
 import os
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-                '/../output/untarBCL/cellranger-tiny-bcl-1_2_0/'
+                '/../output/untarBCL/'
 
-@pytest.mark.untarBCL
-def test_untarBCL():
-    assert os.path.exists(os.path.join(test_output_path, 'RTAComplete.txt'))
+@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

@@ -8,7 +8,12 @@ import os
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/misc/versions/run/'
 
-@pytest.mark.versions
-def test_versions():
+@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'))