From 32b02fa3047c773add9fd837d97951117ccb9557 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 5 Aug 2020 10:27:07 -0500
Subject: [PATCH] Change innerDistance removal for SE to SE matadata check
---
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 0c7285b..34b5a6d 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1026,7 +1026,7 @@ process aggrQC {
# remove inner distance report if it is empty (SE repRID)
echo -e "LOG: removing dummy inner distance file" >> ${repRID}.aggrQC.log
- if [ wc -l ${innerDistance} | awk '{print\${1}}' -eq 0 ]
+ if [ "${endsM}" == "se" ]
then
rm -f ${innerDistance}
fi
@@ -1035,4 +1035,4 @@ process aggrQC {
echo -e "LOG: running multiqc" >> ${repRID}.aggrQC.log
multiqc -c ${multiqcConfig} . -n ${repRID}.multiqc.html
"""
-}
+}
\ No newline at end of file
--
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