Update pipeline.nf

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)