Combine trimData CI se/pe into 1 unit test

.gitlab-ci.yml

@@ -26,19 +26,13 @@ getData:
   - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' sh ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4
   - pytest -m getData
 
-trimData_se:
+trimData:
   stage: unit
   script:
   - if [ `nproc` -gt 8 ]; then ncore=8; else ncore=`nproc`; fi
   - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --basename 16-1ZX4 -j ${ncore} ./test_data/fastq/16-1ZX4.R1.fastq.gz
-  - pytest -m trimData_se
-
-trimData_pe:
-  stage: unit
-  script:
-  - if [ `nproc` -gt 8 ]; then ncore=8; else ncore=`nproc`; fi
   - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA -j ${ncore} ./test_data/fastq/Q-Y5JA.R1.fastq.gz ./test_data/fastq/Q-Y5JA.R2.fastq.gz
-  - pytest -m trimData_pe
+  - pytest -m trimData
 
 integration_se:
   stage: integration

workflow/tests/test_trimData.py

@@ -8,11 +8,8 @@ import os
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../../'
 
-@pytest.mark.trimData_se
-def test_trimData_se():
+@pytest.mark.trimData
+def test_trimData():
     assert os.path.exists(os.path.join(test_output_path, '16-1ZX4_trimmed.fq.gz'))
-
-@pytest.mark.trimData_pe
-def test_trimData_pe():
     assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_R1_val_1.fq.gz'))
     assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_R2_val_2.fq.gz'))
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