From 52b950a60c34e4dcbf64f418bb59d1ac81681b66 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 5 Jan 2021 16:15:31 -0600
Subject: [PATCH] Fix fail pre execution run
---
workflow/conf/aws.config | 4 ++++
workflow/conf/biohpc.config | 8 +++++++-
workflow/nextflow.config | 3 +++
workflow/rna-seq.nf | 9 +--------
4 files changed, 15 insertions(+), 9 deletions(-)
diff --git a/workflow/conf/aws.config b/workflow/conf/aws.config
index 17ed841..cdd91da 100644
--- a/workflow/conf/aws.config
+++ b/workflow/conf/aws.config
@@ -112,6 +112,10 @@ process {
cpus = 1
memory = '1 GB'
}
+ withName:failPreExecutionRun {
+ cpus = 1
+ memory = '1 GB'
+ }
withName:failExecutionRun {
cpus = 1
memory = '1 GB'
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 817a2ab..82ee0f3 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -20,7 +20,7 @@ process {
executor = 'local'
}
withName:trimData {
- queue = '128GB,256GB,256GBv1,384GB'
+ queue = 'super'
}
withName:getRefInfer {
queue = 'super'
@@ -79,6 +79,12 @@ process {
withName:finalizeExecutionRun {
executor = 'local'
}
+ withName:failPreExecutionRun {
+ executor = 'local'
+ }
+ withName:failPreExecutionRun {
+ executor = 'local'
+ }
withName:failExecutionRun {
executor = 'local'
}
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index a226934..a62f9f5 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -88,6 +88,9 @@ process {
withName:finalizeExecutionRun {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
+ withName:failPreExecutionRun {
+ container = 'gudmaprbk/deriva1.3:1.0.0'
+ }
withName:failExecutionRun {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 082aa09..b223f2e 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -374,7 +374,7 @@ process parseMetadata {
# check read counts match for fastqs
fastqReadError=false
fastqReadError_details=""
- if [ "\${endsMeta}" == "pe" ]
+ if [ "\${endsManual}" == "pe" ]
then
r1Count=\$(zcat ${fastq[0]} | wc -l)
r2Count=\$(zcat ${fastq[1]} | wc -l)
@@ -2082,13 +2082,6 @@ process failPreExecutionRun {
hostname > ${repRID}.failPreExecutionRun.log
ulimit -a >> ${repRID}.failPreExecutionRun.log
- executionRun=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Execution_Run/RID=${executionRunRID})
- workflow=\$(echo \${executionRun} | grep -o '\\"Workflow\\":.*\\"Reference' | grep -oP '(?<=\\"Workflow\\":\\").*(?=\\",\\"Reference)')
- genome=\$(echo \${executionRun} | grep -o '\\"Reference_Genome\\":.*\\"Input_Bag' | grep -oP '(?<=\\"Reference_Genome\\":\\").*(?=\\",\\"Input_Bag)')
-
- cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"')
- cookie=\${cookie:11:-1}
-
errorDetails=""
if [ ${fastqCountError} == true ]
then
--
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