Update pipeline.nf

pipeline.nf

@@ -71,44 +71,44 @@ Required arguments:
 Optional arguments:
 
 	--tfbs_path Path to directory with output from tfbsscan. If given tfbsscan will not be run.
-
+	
 	Footprint extraction:
-	--window_length INT	(Default: 200)
-	--step INT		(Default: 100)
-	--percentage INT	(Default: 0)
-
+	--window_length INT	This parameter sets the length of a sliding window. (Default: 200)
+	--step INT		This parameter sets the number of positions to slide the window forward. (Default: 100)
+	--percentage INT	Threshold in percent (Default: 0)
+	
 	Filter unknown motifs:
-	--min_size_fp INT	(Default: 10)
-	--max_size_fp INT	(Default: 100)
-
+	--min_size_fp INT	Minimum sequence length threshold. Smaller sequences are discarded. (Default: 10)
+	--max_size_fp INT	Maximum sequence length threshold. Discards all sequences longer than this value. (Default: 100)
+	
 	Clustering:
 	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 Interations	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:
 	--min_seq INT 		Sets the minimum number of sequences required for the FASTA-files given to GLAM2. (Default: 100)
 	--motif_min_key INT	Minimum number of key positions (aligned columns) in the alignment done by GLAM2. (Default: 8)
 	--motif_max_key INT	Maximum number of key positions (aligned columns) in the alignment done by GLAM2.f (Default: 20)
 	--iteration INT		Number of iterations done by glam2. More Iterations: better results, higher runtime. (Default: 10000)
 	--tomtom_treshold float	Threshold for similarity score. (Default: 0.01)
 	--best_motif INT	Get the best X motifs per cluster. (Default: 3)
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+	
 	Moitf clustering:
 	--cluster_motif	Boolean	If 1 pipeline clusters motifs. If its 0 it does not. (Defaul: 0)
 	--edge_weight INT	Minimum weight of edges in motif-cluster-graph (Default: 5)
 	--motif_similarity_thresh FLOAT	Threshold for motif similarity score (Default: 0.00001)
-
+	
 	Creating GTF:
 	--organism [hg38 | hg19 | mm9 | mm10]	Input organism
 	--tissues List/String 	List of one or more keywords for tissue-/category-activity, categories must be specified as in JSON