Commit 6cef4fe6 authored by Jeremy Mathews's avatar Jeremy Mathews

Add pytest

parent b1e7748e
Pipeline #4425 failed with stages
in 5 minutes and 36 seconds
......@@ -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
#!/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)))
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