From 72ce1955abb8788fb14abdf1b1d3232be884190e Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 13 Mar 2019 08:28:29 -0500
Subject: [PATCH] Add in nextflow version.
---
workflow/main.nf | 1 +
workflow/scripts/generate_versions.py | 2 ++
2 files changed, 3 insertions(+)
diff --git a/workflow/main.nf b/workflow/main.nf
index bc237f9..93334c7 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -508,6 +508,7 @@ process softwareReport {
script:
"""
+ echo $workflow.nextflow.version > version_nextflow.txt
python3 $baseDir/scripts/generate_versions.py -f *.txt -o software_versions
python3 $baseDir/scripts/generate_references.py -r $references -o software_references
"""
diff --git a/workflow/scripts/generate_versions.py b/workflow/scripts/generate_versions.py
index f75a343..d4dd7fb 100644
--- a/workflow/scripts/generate_versions.py
+++ b/workflow/scripts/generate_versions.py
@@ -23,6 +23,7 @@ logger.propagate = False
logger.setLevel(logging.INFO)
SOFTWARE_REGEX = {
+ 'Nextflow': ['version_nextflow.txt', r"(\S+)"],
'Trim Galore!': ['version_trimgalore.txt', r"version (\S+)"],
'Cutadapt': ['version_cutadapt.txt', r"Version (\S+)"],
'BWA': ['version_bwa.txt', r"Version: (\S+)"],
@@ -88,6 +89,7 @@ def main():
out_filename = output + '_mqc.yaml'
results = OrderedDict()
+ results['Nextflow'] = '<span style="color:#999999;\">N/A</span>'
results['Trim Galore!'] = '<span style="color:#999999;\">N/A</span>'
results['Cutadapt'] = '<span style="color:#999999;\">N/A</span>'
results['BWA'] = '<span style="color:#999999;\">N/A</span>'
--
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