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Commit 62e0726d authored by Jeremy Mathews's avatar Jeremy Mathews
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Add CI updates

parent e4c36754
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4 merge requests!53Develop,!51Resolve "Add pytest to CI",!50Resolve "Add pytest to CI",!49Resolve "Add pytest to CI"
Pipeline #4451 failed with stages
in 5 minutes and 4 seconds
......@@ -29,6 +29,10 @@ 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: "$CI_JOB_NAME"
when: always
......@@ -46,6 +50,10 @@ run_mu.cr2v2ref1.2.0:
- tags
script:
- nextflow run workflow/main.nf --fastq "$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
......@@ -62,7 +70,11 @@ run_hu.cr3v3ref3.0.0:
except:
- 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'
- 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
......@@ -72,4 +84,4 @@ run_hu.cr3v3ref3.0.0:
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
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/misc/checkDesignFile/**/'
@pytest.mark.design
def test_design():
assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
#!/usr/bin/env python3
import pytest
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/'
@pytest.mark.count301
def test_count301():
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/count301/'
@pytest.mark.count302
def test_count302():
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/count302/'
#!/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__)) + \
'/../output/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__)) + \
'/../output/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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