pipeline: Added seed for glam2

pipeline.nf

@@ -46,6 +46,7 @@
 	params.motif_max_key = 20 // Maximum number of key positions (aligned columns)
 	params.iteration = 10000 // Number of Iterations done by glam2. A high iteration number equals a more accurate result but with an higher runtime.
 	params.gap_penalty = 1000
+	params.seed = 123456789
 
 	//tomtom
 	params.tomtom_treshold = 0.01 // threshold for similarity score.
@@ -116,6 +117,7 @@ if (params.bigwig == "" || params.bed == "" || params.organism == "" || params.g
 		--tomtom_treshold FLOAT	Threshold for similarity score. (Default: 0.01)
 		--best_motif INT	Get the best X motifs per cluster. (Default: 3)
 		--gap_penalty INT	Set penalty for gaps in GLAM2 (Default: 1000)
+		--seed Set seed for GLAM2 (Default: 123456789)
 		Moitf clustering:
 		--cluster_motif	Boolean	If 1 pipeline clusters motifs. If its 0 it does not. (Defaul: 0)
 		--edge_weight INT	Minimum weight of edges in motif-cluster-graph (Default: 5)
@@ -154,7 +156,7 @@ int_params = ["window_length", "step", "min_size_fp", "max_size_fp", "kmer",
 req_params = ["bigwig", "bed", "genome_fasta", "motif_db", "config"]
 all_params = int_params + req_params + ["organism" , "identity", "tfbsscan_method",
 							"percentage", "tomtom_treshold", "motif_similarity_thresh", "out",
-							"tissues", "gtf_path", "cluster_motif", "tfbs_path", "help", "gtf2"]
+							"tissues", "gtf_path", "cluster_motif", "tfbs_path", "help", "gtf2", "seed"]
 
 valid_organism = ["hg38", "hg19", "mm9", "mm10"]
 valid_tfbsscan_methods = ["moods","fimo"]
@@ -376,7 +378,7 @@ process glam2 {
 
   script:
   """
-  glam2 n ${fasta} -O ./${name}/ -E ${params.gap_penalty} -J ${params.gap_penalty} -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration}
+  glam2 n ${fasta} -O ./${name}/ -E ${params.gap_penalty} -J ${params.gap_penalty} -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration} -s ${params.seed}
   """
 }
 
@@ -505,7 +507,7 @@ process merge_fasta {
 
 	output:
 	file ('*.fasta') into motif_clustered_fasta_list
-  file('*.png')
+  file('*')
 
   when:
   params.cluster_motif == 1
@@ -544,7 +546,7 @@ process clustered_glam2 {
 	script:
   name = fasta.getBaseName()
 	"""
-	glam2 n ${fasta} -O ./${name}/ -E ${params.gap_penalty} -J ${params.gap_penalty} -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration}
+	glam2 n ${fasta} -O ./${name}/ -E ${params.gap_penalty} -J ${params.gap_penalty} -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration} -s ${params.seed}
 	"""
 }
 
@@ -836,4 +838,6 @@ workDir     : ${workflow.workDir}
 exit status : ${workflow.exitStatus}
 Error report: ${workflow.errorReport ?: '-'}
 """
+f = file(workflow.workDir + '/tmp/re_scan_final')
+f.deleteDir()
 }