From 04c81525e419aa4e2bef84db46a6c33c9da0d1a2 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 27 Jan 2021 20:00:38 -0600
Subject: [PATCH] Fix stranded override
---
workflow/rna-seq.nf | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index d1d745c..43aa58e 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1190,12 +1190,17 @@ process checkMetadata {
ulimit -a >> ${repRID}.checkMetadata.log
pipelineError=false
+ pipelineError_ends=false
+ pipelineError_stranded=false
+ pipelineError_spike=false
+ pipelineError_species=false
# check if submitted metadata matches inferred
if [ "${strandedMeta}" != "${strandedInfer}" ]
then
if [ "${params.strandedForce}" != "" ]
then
pipelineError=false
+ pipelineError_stranded=false
echo -e "LOG: stranded forced: Submitted=${strandedMeta}; Inferred=${strandedInfer}" >> ${repRID}.checkMetadata.log
else
pipelineError=true
@@ -1216,6 +1221,7 @@ process checkMetadata {
fi
else
pipelineError=false
+ pipelineError_stranded=false
echo -e "LOG: stranded matches: Submitted=${strandedMeta}; Inferred=${strandedInfer}" >> ${repRID}.checkMetadata.log
fi
if [ "${endsMeta}" != "${endsInfer}" ]
--
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