From 0d9892a8c98d11d211377e67ced9df9d078f9977 Mon Sep 17 00:00:00 2001
From: renewiegandt <rene.wiegandt@mpi-bn.mpg.de>
Date: Fri, 14 Dec 2018 14:09:36 +0100
Subject: [PATCH 1/3] removed echo true from process

---
 pipeline.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pipeline.nf b/pipeline.nf
index b0608be..a078df6 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -239,7 +239,6 @@ if(params.tfbs_path == "") {
 */
 process overlap_with_known_TFBS {
 	conda "${path_env}"
-	echo true
 
 	publishDir "${params.out}/unknown_overlap/"
 

From 651363865bc2040e35f53c2d311c67e679c7b67f Mon Sep 17 00:00:00 2001
From: SebastianBeyvers <Sebastian.Beyvers@mpi-bn.mpg.de>
Date: Fri, 14 Dec 2018 14:29:17 +0100
Subject: [PATCH 2/3] Readme formatted

---
 README.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 131b443..a884632 100644
--- a/README.md
+++ b/README.md
@@ -89,13 +89,13 @@ Optional arguments:
 	--tomtom_treshold float	Threshold for similarity score. (Default: 0.01)
 
 	Motif clustering:
-  --cluster_motif BOOLEAN IF its 1 motifs will be clustered (Default: 0)
+  	--cluster_motif BOOLEAN IF its 1 motifs will be clustered (Default: 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)
+  	--motif_similarity_thresh FLOAT threshold for motif similarity score (Default: 0.00001)
 
-  Creating GTF:
-  --tissue STRING Filter for one or more tissue/category activity, categories as in JSON config (Default: None)
-  --organism STRING Source organism: [ hg19 | hg38 or mm9 | mm10 ] (Default: hg38)
+  	Creating GTF:
+ 	--tissue STRING Filter for one or more tissue/category activity, categories as in JSON config (Default: None)
+  	--organism STRING Source organism: [ hg19 | hg38 or mm9 | mm10 ] (Default: hg38)
 
 All arguments can be set in the configuration files.
  ```

From 8a306b1567104f055f38c714467fc86565efeb08 Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Fri, 14 Dec 2018 14:44:51 +0100
Subject: [PATCH 3/3] $"motifs" falsch -> "$motifs" richtig :)

---
 bin/compareBed.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/compareBed.sh b/bin/compareBed.sh
index 97e4a82..db58a2c 100644
--- a/bin/compareBed.sh
+++ b/bin/compareBed.sh
@@ -226,7 +226,7 @@ Rscript --vanilla $path/maxScore.R "$workdir"/pass1Fa.bed
 #echo "also get subsequences with no overlap of overlapping sequences"
 help=true
 
-if [ -d $"motifs" ]
+if [ -d "$motifs" ]
 then
 for i in "$motifs"/*.bed
 do