From bce4b6eafa4389ff38ffec4a6bb0239350969453 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 19 Jan 2020 00:40:33 -0600
Subject: [PATCH] Keep meta endness separate
---
workflow/rna-seq.nf | 13 +++++++++----
1 file changed, 9 insertions(+), 4 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 6170be7..e0b6cd3 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -131,16 +131,21 @@ process parseMetadata {
echo "LOG: replicate RID metadata parsed: \${rep}" >>${repRID}.parseMetadata.err
# Get endedness metadata
- ends=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p ends)
- echo "LOG: endedness metadata parsed: \${ends}" >>${repRID}.parseMetadata.err
+ endsMeta=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p ends)
+ echo "LOG: endedness metadata parsed: \${endsMeta}" >>${repRID}.parseMetadata.err
# Manually get endness
endsManual=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p endsManual)
echo "LOG: endedness manually detected: \${ends}" >>${repRID}.parseMetadata.err
- if [ \${ends} == "uk" ]
+
+
+ if [ \${endsMeta} == "uk" ]
then
ends=\${endsManual}
- echo "LOG: endness metadata overwitten my manually detected" >>${repRID}.parseMetadata.err
+ echo "LOG: manual detected endness used" >>${repRID}.parseMetadata.err
+ else
+ ends=\${endsMeta}
+ echo "LOG: metadata endness used" >>${repRID}.parseMetadata.err
fi
# Get strandedness metadata
--
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