From 1e6c14ae9b3bbe160293f5feb71af9d458fb3192 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 17 Dec 2020 11:09:15 -0600
Subject: [PATCH] Change Workflow name
---
workflow/nextflow.config | 2 +-
workflow/rna-seq.nf | 8 ++++----
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 9066835..6d91804 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -110,6 +110,6 @@ manifest {
homePage = 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq'
description = 'This pipeline was created to be a standard mRNA-sequencing analysis pipeline which integrates with the GUDMAP and RBK consortium data-hub.'
mainScript = 'rna-seq.nf'
- version = 'v0.1.0_indev'
+ version = 'v0.0.4_indev'
nextflowVersion = '>=19.09.0'
}
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 67dfe6e..cfc9bd8 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1366,7 +1366,7 @@ process uploadExecutionRun {
ulimit -a >> ${repRID}.uploadExecutionRun.log
echo LOG: searching for workflow RID - BICF mRNA ${workflow.manifest.version} >> ${repRID}.uploadExecutionRun.log
- workflow=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Workflow/Name=BICF%20mRNA/Version=${workflow.manifest.version})
+ workflow=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Workflow/Name=BICF%20mRNA%20Replicate/Version=${workflow.manifest.version})
workflow=\$(echo \${workflow} | grep -o '\\"RID\\":\\".*\\",\\"RCT')
workflow=\${workflow:7:-6}
echo LOG: workflow RID extracted - \${workflow} >> ${repRID}.uploadExecutionRun.log
@@ -1391,17 +1391,17 @@ process uploadExecutionRun {
cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"')
cookie=\${cookie:11:-1}
- exist=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Execution_Run/Workflow=\${workflow}/Reference_Genome=\${genome}/Input_Bag=${inputBagRID}/Replicate=${repRID})
+ exist=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Execution_Run/Workflow=\${workflow}/Replicate=${repRID})
echo \${exist} >> ${repRID}.uploadExecutionRun.log
if [ "\${exist}" == "[]" ]
then
- executionRun_rid=\$(python3 uploadExecutionRun.py -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d 'Run in process' -o ${source} -c \${cookie} -u F)
+ executionRun_rid=\$(python3 uploadExecutionRun.py -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s In-progress -d 'Run in process' -o ${source} -c \${cookie} -u F)
echo LOG: execution run RID uploaded - \${executionRun_rid} >> ${repRID}.uploadExecutionRun.log
else
rid=\$(echo \${exist} | grep -o '\\"RID\\":\\".*\\",\\"RCT')
rid=\${rid:7:-6}
echo \${rid} >> ${repRID}.uploadExecutionRun.log
- executionRun_rid=\$(python3 uploadExecutionRun.py -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d 'Run in process' -o ${source} -c \${cookie} -u \${rid})
+ executionRun_rid=\$(python3 uploadExecutionRun.py -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s In-progress -d 'Run in process' -o ${source} -c \${cookie} -u \${rid})
echo LOG: execution run RID updated - \${executionRun_rid} >> ${repRID}.uploadExecutionRun.log
fi
--
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