From 1f7ba7d5564df15fb3633c00613c785268dc9a83 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Jan 2021 20:28:52 -0600
Subject: [PATCH] Fix stranded test
---
workflow/rna-seq.nf | 24 +++++++++++++-----------
1 file changed, 13 insertions(+), 11 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 7cfff2c..c7da457 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -875,19 +875,21 @@ process checkMetadata {
fi
if [ "${strandedMeta}" != "${strandedInfer}" ]
then
- if [ "${strandedMeta}" == "unstranded" ]
- then
- pipelineError=true
- pipelineError_stranded=true
- echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
- elif [ "${strandedInfer}" != "forward"] || [ "${strandedInfer}" != "reverse" ]
+ pipelineError=true
+ pipelineError_stranded=true
+ echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
+ if [ "${strandedMeta}" == "stranded" ]
then
- pipelineError=true
- pipelineError_stranded=true
- echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
+ if [ "${strandedInfer}" == "forward"] || [ "${strandedInfer}" == "reverse" ]
+ then
+ pipelineError=false
+ pipelineError_stranded=false
+ echo -e "LOG: stranded matches: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
+ else
+ echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
+ fi
else
- pipelineError_stranded=false
- echo -e "LOG: stranded matches: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
+ echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
fi
else
pipelineError_stranded=false
--
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