From a1d18adc79ceacd0a2dab6a59bf2c956c816e4dd Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Jan 2021 21:34:08 -0600
Subject: [PATCH] Fix stranded test
---
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 54874a6..97f9462 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -892,10 +892,9 @@ process checkMetadata {
then
pipelineError=true
pipelineError_stranded=true
- echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
if [ "${strandedMeta}" == "stranded" ]
then
- if [ "${strandedInfer}" == "forward"] || [ "${strandedInfer}" == "reverse" ]
+ if [ "${strandedInfer}" == "forward"] | [ "${strandedInfer}" == "reverse" ]
then
pipelineError=false
pipelineError_stranded=false
@@ -907,6 +906,7 @@ process checkMetadata {
echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
fi
else
+ pipelineError=false
pipelineError_stranded=false
echo -e "LOG: stranded matches: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
fi
--
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