Add in intital scripts.

README.md

+To run a set of replicates from study RID:
+------------------------------------------
+Run in repo root dir:
+* `sh scripts/splitStudy.sh [studyRID]`
+It will run in parallel in batches of 5 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`).

scripts/split_study.py

+#!/usr/bin/env python3
+
+import argparse
+import pandas as pd
+import warnings
+warnings.simplefilter(action='ignore', category=FutureWarning)
+
+
+def get_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-s', '--studyRID',
+                        help="The study RID.", required=True)
+    args = parser.parse_args()
+    return args
+
+
+def main():
+    args = get_args()
+    studyRID = pd.read_json(args.studyRID+"_studyRID.json")
+    if studyRID["RID"].count() > 0:
+        studyRID["RID"].to_csv(
+            args.studyRID+"_studyRID.csv", header=False, index=False)
+    else:
+        raise Exception("No associated replicates found: %s" %
+                        studyRID)
+
+
+if __name__ == '__main__':
+    main()

scripts/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 30; done < "$1_studyRID.csv" | xargs -P 5 -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 -with-report ./output/{}_report.html -with-timeline ./output/{}_timeline.html
+
+# cleanup study RID files
+rm $1_studyRID.json
+#rm $1_studyRID.csv