split_study.sh

#!/bin/bash

#SBATCH -p super
#SBATCH --job-name GUDMAP-RBK_Study
#SBATCH -t 7-0:0:0

# 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

# extract replicate RIDs
module load python/3.6.4-anaconda
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 --dev false --upload true --email gervaise.henry@utsouthwestern.edu

# cleanup study RID files
rm $1_studyRID.json
rm $1_studyRID.csv