From afe9eb2bdb341b5c67219c3427ff879ba0b1f402 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= <rene.wiegandt@mpi-bn.mpg.de>
Date: Tue, 4 Dec 2018 08:47:52 -0500
Subject: [PATCH] minor changes

---
 nextflow.config | 4 ----
 pipeline.nf     | 2 ++
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 6f44ba3..2e84338 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,9 +1,5 @@
 createTimeout = 60
 
-params {
-
-}
-
 env {
 	path_bin = $workflow.projectDir/bin
 	path_env = $workflow.projectDir/masterenv.yml
diff --git a/pipeline.nf b/pipeline.nf
index a8e15dc..d8e2669 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -12,6 +12,8 @@ process footprint_extraction {
 	conda "${path_env}"
 
 	tag{name}
+	publishDir '${out}', mode: 'copy', pattern: '*.bed'
+	publishDir '/mnt/agnerds/Rene.Wiegandt/log', mode: 'copy', pattern: '*.log'
 
 	input:
 	set name, file (bigWig), file (bed) from footprint_in