Restructure pytests

.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 test_data/hu.v2s1r500
   - mkdir -p test_data/mu.v2s2r10k
@@ -29,10 +30,7 @@ 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: "$CI_JOB_NAME"
     when: always
@@ -50,10 +48,7 @@ run_mu.cr2v2ref1.2.0:
     - tags
   script:
   - nextflow run workflow/main.nf --fastq "$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
@@ -71,10 +66,7 @@ run_hu.cr3v3ref3.0.0:
     - 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'
-  - pytest -m design
   - pytest -m count302
-  - pytest -m versions
-  - pytest -m multiqc
   artifacts:
     name: "$CI_JOB_NAME"
     when: always

workflow/tests/test_check_design.py

@@ -6,8 +6,12 @@ from io import StringIO
 import os
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-		'/../output/misc/checkDesignFile/**/'
+		'/../output/misc/checkDesignFile/run/'
 
-@pytest.mark.design
-def test_design():
+@pytest.mark.count211
+def test_count211_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

@@ -5,18 +5,16 @@ 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/'
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                    '/../output/'
 
-@pytest.mark.count301
-def test_count301():
-    test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-                    '/../output/count301/'
 
+@pytest.mark.count211
+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.count302
-def test_count302():
-    test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-                    '/../output/count302/'
+def test_count302_count():
+    assert os.path.exists(os.path.join(test_output_path, 'count302', 'sample1_metrics_summary.tsv'))
+    assert os.path.exists(os.path.join(test_output_path, 'count302', 'sample1', 'outs'))

workflow/tests/test_multiqc.py

@@ -6,8 +6,12 @@ from io import StringIO
 import os
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-                '/../output/multiqc/**/'
+                '/../output/multiqc/run/'
 
-@pytest.mark.multiqc
-def test_multiqc():
+@pytest.mark.count211
+def test_count211_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

@@ -6,9 +6,14 @@ from io import StringIO
 import os
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-                '/../output/misc/versions/**/'
+                '/../output/misc/versions/run/'
 
-@pytest.mark.versions
-def test_versions():
+@pytest.mark.count211
+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.count302
+def test_count302_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'))