diff --git a/README.md b/README.md index a4b6f56c897d31aba5740c05c919b00f07979e86..2216c2775a2145f8e021cb221b18414f38ed9304 100644 --- a/README.md +++ b/README.md @@ -62,7 +62,8 @@ 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 25 replicatesRID with 30 second delays between launches. +It will run in parallel in batches of 25 replicatesRID with 30 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`). diff --git a/workflow/scripts/splitStudy.sh b/workflow/scripts/splitStudy.sh index bade44bbdf1c06b0771bf9f0d040d660fa77fe4d..0af729da20cf4facdeb9f7fd611249f215f8f6f6 100644 --- a/workflow/scripts/splitStudy.sh +++ b/workflow/scripts/splitStudy.sh @@ -1,5 +1,11 @@ #!/bin/bash +#SBATCH -p super +#SBATCH --job-name GUDMAP-RBK_Study +#SBATCH -t 7-0:0:0 +#SBATCH -o job_%j.out +#SBATCH -e job_%j.out + # query GUDMAP/RBK for study RID echo "curl --location --request GET 'https://www.gudmap.org/ermrest/catalog/2/entity/RNASeq:Replicate/Study_RID="${1}"'" | bash > $1_studyRID.json