Commit b8223d0a authored by Spencer Barnes's avatar Spencer Barnes
Browse files

Merge branch 'master' into '26-negative-fraglength'

# Conflicts:
#   CHANGELOG.md
parents 481f3f7e 876e2cc6
Pipeline #6130 passed with stages
in 923 minutes and 52 seconds
......@@ -15,6 +15,8 @@ All notable changes to this project will be documented in this file.
- Fix xcor to increase file size for --random-source
- Fix skip diff test for paired-end data
- Fix xcor to get lowest non zero value about 50
- Fix references to display in Multiqc report
## [publish_1.0.6 ] - 2019-05-31
### Added
......
......@@ -654,10 +654,10 @@ process multiqcReport {
"""
echo $workflow.nextflow.version > version_nextflow.txt
singularity exec /project/shared/bicf_workflow_ref/singularity_images/multiqc.sif multiqc --version > version_multiqc.txt
singularity exec /project/shared/bicf_workflow_ref/singularity_images/bicf-multiqc-2.0.0.img multiqc --version > version_multiqc.txt
python --version &> version_python.txt
python3 $baseDir/scripts/generate_references.py -r $references -o software_references
python3 $baseDir/scripts/generate_versions.py -o software_versions
singularity exec /project/shared/bicf_workflow_ref/singularity_images/multiqc.sif multiqc -c $multiqc .
singularity exec /project/shared/bicf_workflow_ref/singularity_images/bicf-multiqc-2.0.0.img multiqc -c $multiqc .
"""
}
......@@ -4,6 +4,7 @@ import pytest
import os
import utils
import yaml
from bs4 import BeautifulSoup
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/multiqcReport/'
......@@ -21,3 +22,14 @@ def test_software_references_output():
data_loaded = yaml.load(stream)
assert len(data_loaded['data'].split('<ul>')) == 19
@pytest.mark.singleend
def test_software_references_html():
multiqc_report = os.path.join(test_output_path, 'multiqc_report.html')
html_file = open(multiqc_report, 'r')
source_code = html_file.read()
multiqc_html = BeautifulSoup(source_code, 'html.parser')
references = multiqc_html.find(id="mqc-module-section-Software_References")
assert references is not None
assert len(references.find_all('ul')) == 18
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