Changed singularity container to allow for rendering of references.

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• CHANGELOG.md is updated

Closes #66 (closed)

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