diff --git a/README.md b/README.md index 6f6581c9647eb5bdac8f0fe660ae1bd8308a7855..7e4ec6cd7fef82462c81eafc7783d98d61d525b8 100644 --- a/README.md +++ b/README.md @@ -79,7 +79,7 @@ To run a set of replicates from study RID: ------------------------------------------ Run in repo root dir: * `sh workflow/scripts/splitStudy.sh [studyRID]` -It will run in parallel in batches of 5 replicatesRID with 30 second delays between launches.\ +It will run in parallel in batches of 5 replicatesRID with 15 second delays between launches.\ NOTE: Nextflow "local" processes for all replicates will run on the node/machine the bash script is launched from... consider running the study script on the BioHPC's SLURM cluster (use `sbatch`). Errors: diff --git a/workflow/scripts/split_study.sh b/workflow/scripts/split_study.sh index e2f45bfb1c02f075e8dd79f6f25e794c1db33613..bf4b40df8ab9c2f2f52d7ae398e0a7cec9feaf10 100644 --- a/workflow/scripts/split_study.sh +++ b/workflow/scripts/split_study.sh @@ -14,8 +14,8 @@ 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 --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 15; done < "$1_studyRID.csv" | xargs -P 10 -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 # cleanup study RID files rm $1_studyRID.json -rm $1_studyRID.csv +#rm $1_studyRID.csv