Remove reports from config and add to split study

workflow/nextflow.config

@@ -97,19 +97,19 @@ process {
 }
 
 trace {
-  enabled = true
-  file = "${params.outDir}/${params.repRID}_trace.txt"
+  enabled = false
+  file = 'trace.txt'
   fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
 }
 
 timeline {
-  enabled = true
-  file = "${params.outDir}/${params.repRID}_timeline.html"
+  enabled = false
+  file = 'timeline.html'
 }
 
 report {
-  enabled = true
-  file = "${params.outDir}/${params.repRID}_report.html"
+  enabled = false
+  file = 'report.html'
 }
 
 tower {

workflow/scripts/split_study.sh

@@ -14,7 +14,7 @@ python3 ./workflow/scripts/split_study.py -s $1
 # run pipeline on replicate RIDs in parallel
 module load nextflow/20.01.0
 module load singularity/3.5.3
-while read repRID; do echo ${repRID}; sleep 30; done < "$1_studyRID.csv" | xargs -P 5 -I {} nextflow -q run workflow/rna-seq.nf --repRID {} --source production --deriva /project/BICF/BICF_Core/shared/gudmap/test_data/auth/credential.json --bdbag /project/BICF/BICF_Core/shared/gudmap/test_data/auth/cookies.txt --dev false --upload true --email gervaise.henry@utsouthwestern.edu
+while read repRID; do echo ${repRID}; sleep 30; done < "$1_studyRID.csv" | xargs -P 5 -I {} nextflow -q run workflow/rna-seq.nf --repRID {} --source production --deriva /project/BICF/BICF_Core/shared/gudmap/test_data/auth/credential.json --bdbag /project/BICF/BICF_Core/shared/gudmap/test_data/auth/cookies.txt --dev false --upload true --email gervaise.henry@utsouthwestern.edu -with-report ./output/{}_report.html -with-timeline ./output/{}_timeline.html
 
 # cleanup study RID files
 rm $1_studyRID.json