diff --git a/workflow/scripts/split_study.sh b/workflow/scripts/split_study.sh index ae163ed6e681b56c3df78f61193396df5414ebef..e2f45bfb1c02f075e8dd79f6f25e794c1db33613 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 15; done < "$1_studyRID.csv" | xargs -P 5 -I {} nextflow -q run workflow/rna-seq.nf --repRID {} --source staging --dev false --upload true --email gervaise.henry@utsouthwestern.edu +while read repRID; do echo ${repRID}; sleep 15; done < "$1_studyRID.csv" | xargs -P 5 -I {} nextflow -q run workflow/rna-seq.nf --repRID {} --source staging --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 # cleanup study RID files rm $1_studyRID.json