Merge pull request #91 from loosolab/estimation_motifs

Estimation motifs

config/create_gtf.config

@@ -1,3 +1,3 @@
 params{
-  tissue=""
+  tissues=""
 }

config/footprint_extraction.config

@@ -2,5 +2,5 @@ params{
 	window_length = 200
 	step = 100
 	percentage = 0
-	max_bp_between = 6
+	gap_penalty = 6
 }

config/motif_estimation.config

@@ -3,9 +3,9 @@ params {
 	min_seq = 10
 
 	//glam2
-	motif_min_len = 8
-	motif_max_len = 20
-	interation = 10000
+	motif_min_key = 8
+	motif_max_key = 20
+	iteration = 10000
 
 	//tomtom
 	tomtom_treshold = 0.01

pipeline.nf

@@ -60,7 +60,7 @@
 
 //creating_gtf
 	params.organism=""
-	params.tissue=""
+	params.tissues=""
 
 if (params.bigwig == "" || params.bed == "" || params.organism == "" || params.genome_fasta == "" || params.motif_db == "" || params.config == "" || "${params.help}" != "0" ){
 log.info """
@@ -144,20 +144,27 @@ int_params = ["window_length", "step", "min_size_fp", "max_size_fp", "kmer",
              "aprox_motif_len", "motif_occurence", "min_seq_length", "global",
              "sequence_coverage", "memory", "throw_away_seq", "strand",
              "min_seq", "motif_min_key", "motif_max_key", "iteration",
-             "edge_weight", "best_motif", "min_gap", "gap_penalty", "edge_weight"]
+             "edge_weight", "best_motif", "min_gap", "gap_penalty", "edge_weight",
+						 "threads", ]
 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"]
 
 valid_organism = ["hg38", "hg19", "mm9", "mm10"]
 valid_tfbsscan_methods = ["moods","fimo"]
 
 params.each { key, value ->
+	if (!(all_params.contains(key))){
+		println("Warning: Parameter $key is unknown. Please check for typos or the parameter list!")
+	}
   if(int_params.contains(key)) {
     if (!("${value}" ==~ /\d+/ )){
       println("ERROR: $key needs to be an Integer")
       System.exit(2)
     }
   }
-  if(req_params.contains(key)) {
+  if(req_params.contains(key) || (key == "gtf_path" && value != "") ) {
     if(!file(value).exists()) {
       println("ERROR: $key not found. Please check the given path.")
       System.exit(2)
@@ -243,12 +250,20 @@ process overlap_with_known_TFBS {
 	script:
 	if(params.tfbs_path == ""){
 		"""
+		if [[ ! -x "${path_bin}/1.2_filter_motifs/compareBed.sh" ]]
+		then
+			chmod +x ${path_bin}/1.2_filter_motifs/compareBed.sh
+		fi
 		python ${path_bin}/1.2_filter_motifs/tfbsscan.py --use ${params.tfbsscan_method} --core ${params.threads} -m ${db} -g ${fasta} -o ./known_tfbs -b ${bed_peaks}
 		${path_bin}/1.2_filter_motifs/compareBed.sh --data ${bed_footprints} --motifs ./known_tfbs --fasta ${fasta} -o ${name}_unknown.bed -min ${params.min_size_fp} -max ${params.max_size_fp}
 		cp -r ./known_tfbs/ ${params.out}/1.2_filter_motifs/
 		"""
 	} else {
 		"""
+		if [[ ! -x "${path_bin}/1.2_filter_motifs/compareBed.sh" ]]
+		then
+			chmod +x ${path_bin}/1.2_filter_motifs/compareBed.sh
+		fi
 		${path_bin}/1.2_filter_motifs/compareBed.sh --data ${bed_footprints} --motifs ${known_tfbs} --fasta ${fasta} -o ${name}_unknown.bed -min ${params.min_size_fp} -max ${params.max_size_fp}
 		"""
 	}