From ede935b2328120eb31aed4e6a32fc95674ea4bd0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= <rene.wiegandt@mpi-bn.mpg.de>
Date: Tue, 8 Jan 2019 07:17:15 -0500
Subject: [PATCH] Update yaml; removed debug code from pipeline; update README

---
 README.md     | 9 ++++++++-
 masterenv.yml | 1 -
 pipeline.nf   | 7 ++-----
 3 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 642e43c..75279af 100644
--- a/README.md
+++ b/README.md
@@ -7,9 +7,16 @@ For further information read the [documentation](https://github.molgen.mpg.de/lo
 ## Dependencies
 * [conda](https://conda.io/docs/user-guide/install/linux.html)
 * [Nextflow](https://www.nextflow.io/)
+* [MEME-Suite](http://meme-suite.org/doc/install.html?man_type=web)
 
 ## Installation
-Start with installing all dependencies listed above (Nextflow, conda) and downloading all files from the [GitHub repository](https://github.molgen.mpg.de/loosolab/masterJLU2018).
+Start with installing all dependencies listed above (Nextflow, conda, MEME-Suite) and downloading all files from the [GitHub repository](https://github.molgen.mpg.de/loosolab/masterJLU2018).
+It is required to set the [enviroment paths for meme-suite](http://meme-suite.org/doc/install.html?man_type=web#installingtar).
+this can be done with following commands:
+```
+export PATH=[meme-suite instalation path]/libexec/meme-[meme-suite version]:$PATH
+export PATH=[meme-suite instalation path]/bin:$PATH
+```
 
 Every other dependency will be automatically  installed by Nextflow using conda. For that a new conda enviroment will be created, which can be found in the from Nextflow created work directory after the first pipeline run.
 It is **not** required to create and activate the enviroment from the yaml-file beforehand.
diff --git a/masterenv.yml b/masterenv.yml
index 98aed97..751964e 100644
--- a/masterenv.yml
+++ b/masterenv.yml
@@ -15,7 +15,6 @@ dependencies:
   - r-stringr
   - r-optparse
   - bioconductor-iranges
-  - meme
   - moods
   - biopython
   - pybedtools
diff --git a/pipeline.nf b/pipeline.nf
index 8358a68..93190a3 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -251,7 +251,6 @@ if(params.tfbs_path == "") {
 */
 process overlap_with_known_TFBS {
 	conda "${path_env}"
-	echo true
 	publishDir "${params.out}/1.2_filter_motifs/compareBed/", mode :'copy'
 
 	input:
@@ -259,13 +258,11 @@ process overlap_with_known_TFBS {
 
 	output:
 	set name, file ("${name}_unknown.bed") into bed_for_reducing
+	file ('*.stats')
 
 	script:
 	motif_list = bed_motifs.toString().replaceAll(/\s|\[|\]/,"")
 	"""
-	echo ${bed_footprints}
-	echo ${motif_path}
-	echo ${fasta}
 	${path_bin}/1.2_filter_motifs/compareBed.sh --data ${bed_footprints} --motifs ${motif_path} --fasta ${fasta} -o ${name}_unknown.bed -min ${params.min_size_fp} -max ${params.max_size_fp}
 	"""
 }
@@ -662,7 +659,7 @@ process create_GTF {
 
 	script:
 	"""
-	python ${path_bin}/3.1_create_gtf/RegGTFExtractor.py ${params.organism} --tissue ${params.tissues} --wd ${path_bin}/3.1_create_gtf/
+	python ${path_bin}/3.1_create_gtf/RegGTFExtractor.py ${params.organism} --tissue ${params.tissues} --wd ${path_bin}/3.1_create_gtf
 	"""
 }