added parameter to list and description

pipeline.nf

@@ -23,10 +23,19 @@ params.config=""
 	params.max_size_fp=100
 
 //clustering
-	params.sequence_coverage=8
-
-	params.kmer=10
-	params.aprox_motif_len=10
+  //reduce_bed
+  params.kmer=10
+  params.aprox_motif_len=10
+  params.motif_occurence=1
+  params.min_seq_length=10
+
+  //cdhit_wrapper
+  params.global=0
+  params.identity=0.8
+  params.sequence_coverage=8
+  params.memory=800
+  params.throw_away_seq=9
+  params.strand=0
 
 //motif_estimation
 	//bed_to_clustered_fasta
@@ -67,9 +76,19 @@ Optional arguments:
 	--max_size_fp INT (Default: 100)
 
 	Clustering:
-	--sequence_coverage INT (Default: 8)
-	--kmer INT (Default: 10)
-	--aprox_motif_len INT (Default: 10)
+	  Sequence preparation/ reduction:
+	  --kmer INT Kmer length (Default: 10)
+	  --aprox_motif_len INT Motif length (Default: 10)
+	  --motif_occurence FLOAT Percentage of motifs over all sequences. Use 1 (Default) to assume every sequence contains a motif.
+	  --min_seq_length INT Remove all sequences below this value. (Default: 10)
+	  
+	  Clustering:
+	  --global INT Global (=1) or local (=0) alignment. (Default: 0)
+	  --identity FLOAT Identity threshold. (Default: 0.8)
+	  --sequence_coverage INT Minimum aligned nucleotides on both sequences. (Default: 8)
+	  --memory INT Memory limit in MB. 0 for unlimited. (Default: 800)
+	  --throw_away_seq INT Remove all sequences equal or below this length before clustering. (Default: 9)
+	  --strand INT Align +/+ & +/- (= 1). Or align only +/+ (= 0). (Default: 0)
 
 	Motif estimation:
 	--motif_min_len INT	Minimum length of Motif (Default: 8)