Fix fail pre execution run

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'

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'
   }

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'
   }

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