From 7a76914b67ad674c23b662d250a797beecdd3cdb Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 12 Feb 2020 01:52:11 -0600
Subject: [PATCH] Changed singularity container to allow for rendering of
references.
---
CHANGELOG.md | 1 +
workflow/main.nf | 4 ++--
workflow/tests/test_generate_software_references.py | 12 ++++++++++++
3 files changed, 15 insertions(+), 2 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b2f7b74..77ccac2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ All notable changes to this project will be documented in this file.
- Make gtf and geneName files as param inputs
- Fix xcor to increase file size for --random-source
- Fix skip diff test for paired-end data
+- Fix references to display in Multiqc report
## [publish_1.0.6 ] - 2019-05-31
### Added
diff --git a/workflow/main.nf b/workflow/main.nf
index bf87941..1edf9f5 100644
--- a/workflow/main.nf
+++ b/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 .
"""
}
diff --git a/workflow/tests/test_generate_software_references.py b/workflow/tests/test_generate_software_references.py
index 4d0025d..2420c6f 100644
--- a/workflow/tests/test_generate_software_references.py
+++ b/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
--
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