From dc85dfdda9b0a2c2e3b742c69616d8d1eea3e96b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Jan 2021 12:29:30 -0600
Subject: [PATCH] Give split study full path to credentials
---
workflow/scripts/split_study.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflow/scripts/split_study.sh b/workflow/scripts/split_study.sh
index ae163ed..e2f45bf 100644
--- a/workflow/scripts/split_study.sh
+++ b/workflow/scripts/split_study.sh
@@ -14,7 +14,7 @@ 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
+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
# cleanup study RID files
rm $1_studyRID.json
--
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