From 6d5c604c2950e90ab7f12bd4822f8e2e5cafa0f9 Mon Sep 17 00:00:00 2001
From: renewiegandt <rene.wiegandt@mpi-bn.mpg.de>
Date: Wed, 19 Dec 2018 12:18:08 +0100
Subject: [PATCH] adaption of pipeline.nf to changes in bed_to_fasta.R

---
 pipeline.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pipeline.nf b/pipeline.nf
index a39616a..463a790 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -283,7 +283,7 @@ process reduce_bed {
 	"""
 	Rscript ${path_bin}/reduce_bed.R -i ${bed} -k ${params.kmer} -m ${params.aprox_motif_len} -o ${name}_reduced.bed -t ${params.threads} -f ${params.motif_occurence} -s ${params.min_seq_length}
 	"""
-}
+}String
 
 
 /*
@@ -324,7 +324,7 @@ process bed_to_clustered_fasta {
 
     script:
     """
-    Rscript ${path_bin}/bed_to_fasta.R ${bed} ${name} ${params.min_seq}
+    Rscript ${path_bin}/bed_to_fasta.R -i ${bed} -p ${name} -m ${params.min_seq}
     """
 }