Update split study

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:

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