From 09eb019edca2499d806ff4d55398d3ac26ea9ee0 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 7 Jan 2021 22:39:19 -0600
Subject: [PATCH] Update split study
---
README.md | 2 +-
workflow/scripts/split_study.sh | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index 6f6581c..7e4ec6c 100644
--- a/README.md
+++ b/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:
diff --git a/workflow/scripts/split_study.sh b/workflow/scripts/split_study.sh
index e2f45bf..bf4b40d 100644
--- a/workflow/scripts/split_study.sh
+++ b/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
--
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