From 8a404d505d1e1edecd3512b26d4e68889e20427f Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 3 Aug 2020 16:08:36 -0500
Subject: [PATCH] Fix input of parse read length
---
workflow/rna-seq.nf | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 57f3e9a..e09a1d7 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -238,7 +238,11 @@ process parseMetadata {
echo -e "LOG: species metadata parsed: \${species}" >> ${repRID}.parseMetadata.log
# get read length metadata
- readLength=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experiment}" -p readLength)
+ readLength=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p readLength)
+ if [ "\${readLength}" == "nan"]
+ then
+ readLength="Not Entered"
+ fi
echo -e "LOG: read length metadata parsed: \${readLength}" >> ${repRID}.parseMetadata.log
# save design file
--
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