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

# Conflicts:
#   CHANGELOG.md

CHANGELOG.md

@@ -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

workflow/main.nf

@@ -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 .
   """
 }

workflow/tests/test_generate_software_references.py

@@ -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