From a5259fd25ad535a719cd4384744fc2eb732244e1 Mon Sep 17 00:00:00 2001
From: renewiegandt <rene.wiegandt@mpi-bn.mpg.de>
Date: Mon, 3 Dec 2018 14:59:34 +0100
Subject: [PATCH] added parameter to pipeline

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

diff --git a/pipeline.nf b/pipeline.nf
index 548db47..215ba10 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -116,7 +116,7 @@ process glam2 {
 
     script:
     """
-    glam2 n ${fasta} -O . -a 10 -b 20 -z 5
+    glam2 n ${fasta} -O . -a ${params.motif_min_len} -b ${params.motif_max_len} -z 5
     """
 }
 
@@ -138,7 +138,7 @@ process tomtom {
 
     script:
     """
-    tomtom ${meme} ${jaspar_db} -thresh 0.01 -text --norc | sed '/^#/ d' | sed '/^\$/d' > ${name}_known_motif.tsv
+    tomtom ${meme} ${jaspar_db} -thresh ${params.tomtom_treshold} -text --norc | sed '/^#/ d' | sed '/^\$/d' > ${name}_known_motif.tsv
     """
 }