From 080ca18220f5f7fd96b121c8e3ffb0cd360b07d3 Mon Sep 17 00:00:00 2001
From: Harry Hung <4848896+HarryHung@users.noreply.github.com>
Date: Wed, 8 Mar 2023 09:57:31 +0000
Subject: [PATCH] Temp work dir stays in pipeline directory

Former-commit-id: 335f86bace79189a51dc80e2ec87ef2ba0f0eb65
---
 run_pipeline | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/run_pipeline b/run_pipeline
index 1f0b996..ec344a8 100755
--- a/run_pipeline
+++ b/run_pipeline
@@ -4,4 +4,4 @@
 
 pipelineDir=$(dirname -- "$(readlink -f -- "$0")")
 
-$pipelineDir/nextflow -C $pipelineDir/nextflow.config run $pipelineDir/main.nf "$@"
\ No newline at end of file
+$pipelineDir/nextflow -C $pipelineDir/nextflow.config run -w $pipelineDir/work $pipelineDir/main.nf "$@"
\ No newline at end of file