From b769d49f6506b47915bf32821a00aed1603f9f82 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 6 Dec 2018 12:43:58 +0100
Subject: [PATCH] new clustering parameter added

---
 config/cluster.config | 14 ++++++++++++--
 pipeline.nf           |  4 ++--
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/config/cluster.config b/config/cluster.config
index 3dce063..2a1828c 100644
--- a/config/cluster.config
+++ b/config/cluster.config
@@ -1,7 +1,17 @@
 params{
-  sequence_coverage=8
+  threads=1  
 
+  //reduce_bed
   kmer=10
   aprox_motif_len=10
-  threads=1
+  motif_occurence=1
+  min_seq_length=10
+
+  //cdhit_wrapper
+  global=0
+  identity=0.8
+  sequence_coverage=8
+  memory=800
+  throw_away_seq=9
+  strand=0
 }
diff --git a/pipeline.nf b/pipeline.nf
index 5ed2eac..1fabdc3 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -75,7 +75,7 @@ process reduce_bed {
 
 	script:
 	"""
-	Rscript ${path_bin}/reduce_bed.R -i ${bed} -k ${params.kmer} -m ${params.aprox_motif_len} -o ${name}_reduced.bed -t ${params.threads}
+	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}
 	"""
 }
 
@@ -91,7 +91,7 @@ process clustering {
 
 	script:
 	"""
-	Rscript ${path_bin}/cdhit_wrapper.R -i ${bed} -A ${params.sequence_coverage} -o ${name}_clusterd.bed
+	Rscript ${path_bin}/cdhit_wrapper.R -i ${bed} -A ${params.sequence_coverage} -o ${name}_clusterd.bed -c ${params.identity} -G ${params.global} -M ${params.memory} -l ${params.throw_away_seq} -r ${params.strand} -T ${params.threads}
 	"""
 }