Allow study script to run on cluster

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`).
 
 
 

workflow/scripts/splitStudy.sh

 #!/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