fix

bin/compareBed.sh

@@ -267,9 +267,6 @@ fi
 
 Rscript --vanilla $path/merge.R $min $max $workdir $data
 
-echo "------------------------------------------------------------"
-echo $workdir
-head -100 $workdir/merged.bed
 #5. add fasta sequences to bed and create fasta file
 bedtools getfasta -fi $fasta -bed $workdir/merged.bed -bedOut > $output
 bedtools getfasta -name -fi $fasta -bed "$output" -fo "$output".fasta

config/motif_estimation.config

@@ -1,6 +1,6 @@
 params {
 	//bed_to_clustered_fasta
-	min_seq = 50
+	min_seq = 10
 
 	//glam2
 	motif_min_len = 8

nextflow.config

@@ -1,5 +1,5 @@
 wd = "/mnt/agnerds/Rene.Wiegandt/10_Master/masterJLU2018"
-createTimeout = 60
+createTimeout = 40
 params.threads=60 //Parameter for for scripts! Not for nextflow processes.
 params.config="${wd}/config/uropa.config"
 

pipeline.nf

@@ -247,12 +247,12 @@ process overlap_with_known_TFBS {
 	set name, file (bed_footprints), val (bed_motifs), file (fasta) from for_overlap
 
 	output:
-	set name, file ("${name}.bed") into bed_for_reducing
+	set name, file ("${name}_unknown.bed") into bed_for_reducing
 
 	script:
 	motif_list = bed_motifs.toString().replaceAll(/\s|\[|\]/,"")
 	"""
-	${path_bin}/compareBed.sh --data ${bed_footprints} --motifs ${motif_path} --fasta ${fasta} -o ${name}_un.bed -min ${params.min_size_fp} -max ${params.max_size_fp} -p ${path_bin}
+	${path_bin}/compareBed.sh --data ${bed_footprints} --motifs ${motif_path} --fasta ${fasta} -o ${name}_unknown.bed -min ${params.min_size_fp} -max ${params.max_size_fp} -p ${path_bin}
 	"""
 }