From 884ffb3f7e8069300d2358b0971cec98397920ed Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Thu, 7 Jan 2021 23:28:17 -0600 Subject: [PATCH] Remove reports from config and add to split study --- workflow/nextflow.config | 12 ++++++------ workflow/scripts/split_study.sh | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/workflow/nextflow.config b/workflow/nextflow.config index 8ee8989..8828d1a 100644 --- a/workflow/nextflow.config +++ b/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 { diff --git a/workflow/scripts/split_study.sh b/workflow/scripts/split_study.sh index 8ae2def..aeec0fa 100644 --- a/workflow/scripts/split_study.sh +++ b/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 -- GitLab