From 1e3b771493d084fd651025d16c845316a8deac2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= <rene.wiegandt@mpi-bn.mpg.de>
Date: Fri, 14 Dec 2018 18:38:57 -0500
Subject: [PATCH] minor changes

---
 pipeline.nf | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/pipeline.nf b/pipeline.nf
index c20c277..5cd3c8c 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -8,6 +8,8 @@ params.motif_db=""
 params.config=""
 params.tfbs_path=""
 
+params.create_known_tfbs_path = "./"
+
 //peak_calling
 	params.window_length = 200
 	params.step = 100
@@ -55,8 +57,6 @@ params.tfbs_path=""
 	params.organism="hg38"
 	params.tissue=""
 
-	params.tmpdir = "./"
-
 if (params.bigwig == "" || params.bed == "" || params.genome_fasta == "" || params.motif_db == "" || params.config == ""){
 log.info """
 Usage: nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file]
@@ -65,7 +65,10 @@ Required arguments:
 	--bigwig	Path to BigWig-file
 	--bed	Path to BED-file
 	--genome_fasta	Path to genome in FASTA-format
-	--jaspar_db	Path to motif-database in MEME-format
+	--motif_db	Path to motif-database in MEME-format
+	--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: './')
 
 
 Optional arguments:
@@ -101,13 +104,14 @@ Optional arguments:
 	--motif_max_len INT	Maximum length of Motif (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:
 	--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 [homo_sapiens | mus_musculus]
+	--organism [hg38 | hg19 | mm9 | mm10]
 	--tissues
 
 All arguments can be set in the configuration files.
@@ -217,7 +221,7 @@ process extract_known_TFBS {
 
 	script:
 	"""
-	python ${path_bin}/tfbsscan.py --use moods --core ${params.threads} -m ${db} -g ${fasta} -o ${params.tmpdir}
+	python ${path_bin}/tfbsscan.py --use moods --core ${params.threads} -m ${db} -g ${fasta} -o ${params.create_known_tfbs_path}
 	"""
 }
 
@@ -226,7 +230,7 @@ Sets path to known tfbs BED-files. If tfbs_path is set the process extract_known
 */
 if(params.tfbs_path == "") {
 	bed_for_overlap_with_TFBS.combine(known_TFBS_for_overlap.toList()).combine(fa_overlap_2).set {for_overlap}
-	motif_path = params.tmpdir
+	motif_path = params.create_known_tfbs_path
 } else {
 	Channel.from('skipped').set {workaround}
 	bed_for_overlap_with_TFBS.combine(workaround).combine(fa_overlap_2).set {for_overlap}