From 502328a72647d59f3e9761cc601119ee5347246d Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 27 Jan 2021 16:18:04 -0600
Subject: [PATCH] Fix params
---
workflow/rna-seq.nf | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 32e3c26..69c3a2d 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -138,7 +138,7 @@ process trackStart {
}' \
"https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
- if [ ${prarams.track} == true ]
+ if [ ${params.track} == true ]
then
curl -H 'Content-Type: application/json' -X PUT -d \
'{ \
@@ -1442,7 +1442,7 @@ process uploadExecutionRun {
echo "\${executionRun_rid}" > executionRunRID.csv
- if [ ${prarams.track} == true ]
+ if [ ${params.track} == true ]
then
curl -H 'Content-Type: application/json' -X PUT -d \
'{ \
@@ -2056,7 +2056,7 @@ process aggrQC {
multiqc -c ${multiqcConfig} . -n ${repRID}.multiqc.html
cp ${repRID}.multiqc_data/multiqc_data.json ${repRID}.multiqc_data.json
- if [ ${prarams.track} == true ]
+ if [ ${params.track} == true ]
then
curl -H 'Content-Type: application/json' -X PUT -d \
@./${repRID}.multiqc_data.json \
@@ -2345,7 +2345,7 @@ process finalizeExecutionRun {
rid=\$(python3 ${script_uploadExecutionRun_finalizeExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Success -d 'Run Successful' -o ${source} -c \${cookie} -u ${executionRunRID})
echo LOG: execution run RID marked as successful - \${rid} >> ${repRID}.finalizeExecutionRun.log
- if [ ${prarams.track} == true ]
+ if [ ${params.track} == true ]
then
dt=`date +%FT%T.%3N%:z`
curl -H 'Content-Type: application/json' -X PUT -d \
@@ -2450,7 +2450,7 @@ process failPreExecutionRun {
echo "\${rid}" > executionRunRID.csv
- if [ ${prarams.track} == true ]
+ if [ ${params.track} == true ]
then
dt=`date +%FT%T.%3N%:z`
curl -H 'Content-Type: application/json' -X PUT -d \
@@ -2552,7 +2552,7 @@ process failExecutionRun {
echo LOG: execution run RID marked as error - \${rid} >> ${repRID}.failExecutionRun.log
fi
- if [ ${prarams.track} == true ]
+ if [ ${params.track} == true ]
then
dt=`date +%FT%T.%3N%:z`
curl -H 'Content-Type: application/json' -X PUT -d \
--
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