Commit 6955255a authored by Jeremy Mathews's avatar Jeremy Mathews

Add tests for all sections of pipeline

parent 83688779
Pipeline #4445 failed with stages
in 2 minutes and 1 second
......@@ -28,7 +28,12 @@ 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
artifacts:
name: "$CI_JOB_NAME"
when: always
......@@ -44,7 +49,12 @@ simple_2FC:
stage: simple
script:
- nextflow run workflow/main.nf --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv"
- pytest -m design
- pytest -m untarBCL
- pytest -m mkfastq
- pytest -m fastqc
- pytest -m versions
- pytest -m multiqc
artifacts:
name: "$CI_JOB_NAME"
when: always
......
#!/usr/bin/env python3
import pytest
import pandas as pd
from io import StringIO
import os
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../test/misc/checkDesignFile/**/'
@pytest.mark.design
def test_design():
assert os.path.exists(os.path.join(test_output_path, design.checked.csv))
......@@ -4,13 +4,12 @@ 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/**/outs/fastq_path/**/**/'
'/../../test/misc/fastqc/**/**/'
@pytest.mark.fastqc
def test_fastqc_output():
fastqcs = glob.glob('/../../test/mkfastq/*/outs/fastq_path/*/*/*.fastq.gz', recursive=True)
def test_fastqc():
fastqcs = glob.glob('/../../test/misc/fastqc/*/*/*fastqc.zip', recursive=True)
for f in fastqcs:
assert os.path.exists(os.path.join(test_output_path, f))
#!/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/**/outs/fastq_path/**/**/'
@pytest.mark.mkfastq
def test_mkfastq():
fastqcs = glob.glob('/../../test/mkfastq/*/outs/fastq_path/*/*/*.fastq.gz', recursive=True)
for f in fastqcs:
assert os.path.exists(os.path.join(test_output_path, f))
#!/usr/bin/env python3
import pytest
import pandas as pd
from io import StringIO
import os
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../test/multiqc/**/'
@pytest.mark.multiqc
def test_multiqc():
assert os.path.exists(os.path.join(test_output_path, multiqc_report.html))
#!/usr/bin/env python3
import pytest
import pandas as pd
from io import StringIO
import os
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../test/untarBCL/**/'
@pytest.mark.untarBCL
def test_untarBCL():
assert os.path.exists(os.path.join(test_output_path, RTAComplete.txt))
#!/usr/bin/env python3
import pytest
import pandas as pd
from io import StringIO
import os
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../test/misc/versions/**/'
@pytest.mark.versions
def test_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))
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