Merge branch 'master' of https://github.molgen.mpg.de/loosolab/master…

…JLU2018

README.md

@@ -41,7 +41,7 @@ When the enviroment is created, set the variable 'path_env' in the configuration
 
 ## Quick Start
 ```console
-nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file]
+nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --config [UROPA-config-file]
 ```
 ## Parameters
 For a detailed overview for all parameters follow this [link](https://github.molgen.mpg.de/loosolab/masterJLU2018/wiki/Configuration).
@@ -54,47 +54,50 @@ Required arguments:
 	--config		 Path to UROPA configuration file
 	--create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored.
 				 Path can be set as tfbs_path in next run. (Default: './')
+	--out			 Output Directory (Default: './out/')	
+	
 Optional arguments:
-
-	--tfbs_path Path to directory with output from tfbsscan. If given tfbsscan will not be run.
 	
+	--help [0|1]		1 to show this help message. (Default: 0)
+	--tfbs_path 		Path to directory with output from tfbsscan. If given tfbsscan will not be run.
+
 	Footprint extraction:
 	--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	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)
-	
+
 	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

pipeline.nf

@@ -9,6 +9,7 @@
 	params.tfbs_path=""
 	params.create_known_tfbs_path = "./"
 	params.help = 0
+	params.out = "./out/"
 
 //peak_calling
 	params.window_length = 200
@@ -57,9 +58,9 @@
 	params.organism="hg38"
 	params.tissue=""
 
-if (params.bigwig == "" || params.bed == "" || params.genome_fasta == "" || params.motif_db == "" || params.config == "" || "${params.help}" == "1"){
+if (params.bigwig == "" || params.bed == "" || params.genome_fasta == "" || params.motif_db == "" || params.config == "" || "${params.help}" != "0"){
 log.info """
-Usage: nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file]
+Usage: nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --config [UROPA-config-file]
 
 Required arguments:
 	--bigwig		 Path to BigWig-file
@@ -69,9 +70,12 @@ Required arguments:
 	--config		 Path to UROPA configuration file
 	--create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored.
 				 Path can be set as tfbs_path in next run. (Default: './')
+	--out			 Output Directory (Default: './out/')	
+	
 Optional arguments:
-
-	--tfbs_path Path to directory with output from tfbsscan. If given tfbsscan will not be run.
+	
+	--help [0|1]		1 to show this help message. (Default: 0)
+	--tfbs_path 		Path to directory with output from tfbsscan. If given tfbsscan will not be run.
 
 	Footprint extraction:
 	--window_length INT	This parameter sets the length of a sliding window. (Default: 200)