From 412d92df3b7afce4a24e516690c2b762a7bba6d0 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 13 Aug 2020 10:00:21 -0500
Subject: [PATCH] Make by study script run nextflow with quiet flag
---
workflow/scripts/splitStudy.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflow/scripts/splitStudy.sh b/workflow/scripts/splitStudy.sh
index 6552e7d..be4259c 100644
--- a/workflow/scripts/splitStudy.sh
+++ b/workflow/scripts/splitStudy.sh
@@ -10,7 +10,7 @@ python3 ./workflow/scripts/splitStudy.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 10; done < "$1_studyRID.csv" | xargs -P 25 -I {} nextflow run workflow/rna-seq.nf --repRID {}
+while read repRID; do echo ${repRID}; sleep 10; done < "$1_studyRID.csv" | xargs -P 25 -I {} nextflow -q run workflow/rna-seq.nf --repRID {}
# cleanup study RID files
rm $1_studyRID.json
--
GitLab