From 2464b2cb59fd479b31d73196405e656c8078083b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 19 Jan 2021 22:55:31 -0600
Subject: [PATCH] Fix endsManual assignment
---
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 d45ae8b..3178a33 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -344,7 +344,11 @@ process parseMetadata {
fi
# ganually get endness
- endsManual=${fastqCount}
+ if [ "${fastqCount}" == "1" ]
+ endsManual="se"
+ else
+ endsManual="pe"
+ fi
echo -e "LOG: endedness manually detected: ${fastqCount}" >> ${repRID}.parseMetadata.log
# get strandedness metadata
--
GitLab