From 7c606bacad7e7fb0eb15fa699076543b99bd511b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 7 Jan 2021 16:20:20 -0600
Subject: [PATCH] Fix infer metadata
---
workflow/rna-seq.nf | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index e3cbcbe..a17b8bc 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -804,6 +804,7 @@ process inferMetadata {
echo -e "LOG: inference of strandedness results is: \${spike}" >> ${repRID}.inferMetadata.log
speciesError=false
+ speciesError_details=""
# determine species
if [ 1 -eq \$(echo \$(expr \${align_hu} ">=" 40)) ] && [ 1 -eq \$(echo \$(expr \${align_mo} "<" 40)) ]
then
@@ -840,7 +841,7 @@ process inferMetadata {
fi
fi
- if [ "\${speciesError" == false ] && [ "${speciesForce}" = "" ]
+ if [ \${speciesError} ] && [ "${speciesForce}" = "" ]
then
# infer experimental setting from dedup bam
echo -e "LOG: infer experimental setting from dedup bam" >> ${repRID}.inferMetadata.log
--
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