From 37a1345e5a4e867f3af3f6ea3a5f3db8d53feefa Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 28 Jan 2021 16:34:35 -0600
Subject: [PATCH] Convert blank nan submitted metadata to No value
---
workflow/rna-seq.nf | 12 ++++++++++++
1 file changed, 12 insertions(+)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 78a50b1..b0e2c66 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -375,6 +375,10 @@ process parseMetadata {
# get strandedness metadata
stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p stranded)
echo -e "LOG: strandedness metadata parsed: \${stranded}" >> ${repRID}.parseMetadata.log
+ if [ "\${stranded}" == "nan" ]
+ then
+ stranded="_No value_"
+ fi
if [ "${strandedForce}" != "" ]
then
stranded=${strandedForce}
@@ -384,6 +388,10 @@ process parseMetadata {
# get spike-in metadata
spike=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p spike)
echo -e "LOG: spike-in metadata parsed: \${spike}" >> ${repRID}.parseMetadata.log
+ if [ "\${spike}" == "nan" ]
+ then
+ spike="_No value_"
+ fi
if [ "${spikeForce}" != "" ]
then
spike=${spikeForce}
@@ -412,6 +420,10 @@ process parseMetadata {
# get species metadata
species=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experiment}" -p species)
echo -e "LOG: species metadata parsed: \${species}" >> ${repRID}.parseMetadata.log
+ if [ "\${species}" == "nan" ]
+ then
+ species="_No value_"
+ fi
# get read length metadata
readLength=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p readLength)
--
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