From 6bedccc47b1982342c20c4125e02ae9ec1a8d756 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 30 Jan 2020 13:43:47 -0600
Subject: [PATCH] Move endsManual in parseMetadata process from spike to
stranded
---
workflow/rna-seq.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 6c3622b..21c77a0 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -140,11 +140,11 @@ process parseMetadata {
echo "LOG: endedness manually detected: \${endsManual}" >>${repRID}.parseMetadata.err
# Get strandedness metadata
- stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p stranded)
+ stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p stranded -e \${endsManual})
echo "LOG: strandedness metadata parsed: \${stranded}" >>${repRID}.parseMetadata.err
# Get spike-in metadata
- spike=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p spike -e \${endsManual})
+ spike=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p spike)
echo "LOG: spike-in metadata parsed: \${spike}" >>${repRID}.parseMetadata.err
# Get species metadata
--
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