Add pytest

.gitlab-ci.yml

@@ -28,6 +28,7 @@ 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 fastqc
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -43,6 +44,7 @@ simple_2FC:
   stage: simple
   script:
     - nextflow run workflow/main.nf --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv"
+    - pytest -m fastqc
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -52,4 +54,4 @@ simple_2FC:
   retry:
     max: 2
     when:
-      - always
\ No newline at end of file
+      - always

workflow/tests/test_fastqc.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/'
+
+@pytest.mark.fastqc
+def test_fastqc_output():
+    assert os.path.exists(os.path.join(test_output_path, glob.glob('*.fastq.gz', recursive=True)))