From f5c550ab78a5eedc803efcd153a1b580a965b483 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 29 Dec 2020 16:53:25 -0600
Subject: [PATCH] Use the right script for upload QC
---
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 0d3f57d..bd1aee4 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -58,7 +58,7 @@ fastqsForce = params.fastqsForce
speciesForce = params.speciesForce
email = params.email
-// Define fixed files
+// Define fixed files and
replicateExportConfig = Channel.fromPath("${baseDir}/conf/Replicate_For_Input_Bag.json")
executionRunExportConfig = Channel.fromPath("${baseDir}/conf/Execution_Run_For_Output_Bag.json")
if (params.source == "dev") {
@@ -1476,7 +1476,7 @@ process uploadQC {
echo LOG: all old mRNA QC RIDs deleted >> ${repRID}.uploadQC.log
fi
- qc_rid=\$(python3 ${script_deleteEntry_uploadQC} -r ${repRID} -e ${executionRunRID} -p "\${end}" -s ${stranded} -l ${length} -w ${rawCount} -f ${finalCount} -o ${source} -c \${cookie} -u F)
+ qc_rid=\$(python3 ${script_uploadQC} -r ${repRID} -e ${executionRunRID} -p "\${end}" -s ${stranded} -l ${length} -w ${rawCount} -f ${finalCount} -o ${source} -c \${cookie} -u F)
echo LOG: mRNA QC RID uploaded - \${qc_rid} >> ${repRID}.uploadQC.log
echo \${qc_rid} > qcRID.csv
--
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