From eb4b1b5afd202ce7e4079ff1823131b2ffe494b2 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 28 Dec 2020 14:24:01 -0600
Subject: [PATCH] Fix exists in upload processed file process
---
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 1f0a4b2..85a504f 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1135,7 +1135,7 @@ process dataQC {
output:
path "${repRID}_tin.hist.tsv" into tinHist
path "${repRID}_tin.med.csv" into tinMedInfer_fl
- path "${repRID}.insertSize.inner_distance_freq.txt" into innerDistance
+ path "${repRID}_insertSize.inner_distance_freq.txt" into innerDistance
script:
"""
@@ -1531,7 +1531,7 @@ process uploadProcessedFile {
exist=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=${repRID})
if [ "\${exist}" != "[]" ]
then
- rids=\$(echo $exist | grep -o '\\"RID\\":\\".\\{7\\}' | sed 's/^.\\{7\\}//')
+ rids=\$(echo \${exist} | grep -o '\\"RID\\":\\".\\{7\\}' | sed 's/^.\\{7\\}//')
for rid in \${rids}
do
python3 deleteEntry.py -r \${rid} -t Processed_File -o ${source} -c \${cookie}
--
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