From 960e0e4ffb2d3033e042ed960a29de8035b5353b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 19 Jan 2020 10:27:04 -0600
Subject: [PATCH] Add ends used to log
---
workflow/rna-seq.nf | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 3a6918b..b279e51 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -139,14 +139,13 @@ process parseMetadata {
endsManual=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p endsManual)
echo "LOG: endedness manually detected: \${endsManual}" >>${repRID}.parseMetadata.err
-
if [ '\${endsMeta}' == 'uk' ]
then
ends=\${endsManual}
- echo "LOG: manual detected endness used" >>${repRID}.parseMetadata.err
+ echo "LOG: manual detected endness used: \${ends}" >>${repRID}.parseMetadata.err
else
ends=\${endsMeta}
- echo "LOG: metadata endness used" >>${repRID}.parseMetadata.err
+ echo "LOG: metadata endness used: \${ends}" >>${repRID}.parseMetadata.err
fi
# Get strandedness metadata
--
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