diff --git a/README.md b/README.md index 23b24d840c661ec6f8c1694629b9024bf9b07caa..399f0daaf0c11acdb1bd1d553a8290d238ac53f1 100644 --- a/README.md +++ b/README.md @@ -62,7 +62,7 @@ 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 +It will run in parallel in batches of 25 replicatesRID with 10 second delays between launches. diff --git a/workflow/scripts/splitStudy.sh b/workflow/scripts/splitStudy.sh index a64b6d9e4cde818d1c6f91fd84144b821febc536..6552e7de2cfe3b5dfabf9cfe82b5a44bc48b3431 100644 --- a/workflow/scripts/splitStudy.sh +++ b/workflow/scripts/splitStudy.sh @@ -10,7 +10,7 @@ python3 ./workflow/scripts/splitStudy.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}; done < "$1_studyRID.csv" | xargs -P 5 -I {} nextflow run workflow/rna-seq.nf --repRID {} +while read repRID; do echo ${repRID}; sleep 10; done < "$1_studyRID.csv" | xargs -P 25 -I {} nextflow run workflow/rna-seq.nf --repRID {} # cleanup study RID files rm $1_studyRID.json