bug fix

bin/merge_similar_clusters.R

@@ -1,7 +1,7 @@
 #!/usr/bin/env Rscript
 
 # Merging FASTA-files, which motifs are similar.
-# 
+#
 # @parameter tsv_in <string> Path to TSV file generated by Tomtom.
 #                            The input for Tomtom is a from all clusters merged meme-file.
 # @parameter file_list <string> Numerically sorted whitespace separated list of absolute fasta-file paths
@@ -10,7 +10,7 @@
 
 args = commandArgs(trailingOnly = TRUE)
 
-tsv_in <- args[1] 
+tsv_in <- args[1]
 file_list <- args[2]
 min_weight <- args[3]
 
@@ -38,7 +38,7 @@ edgelist <- sim_not_unique[query_cluster != target_cluster]
 g <- igraph::graph_from_edgelist(as.matrix(edgelist))
 # converting graph to adjacency matrix
 adj_matrix <- igraph::get.adjacency(g, names = T)
-# generating weighted graph from adjacency matrix 
+# generating weighted graph from adjacency matrix
 g_adj <- igraph::graph_from_adjacency_matrix(adj_matrix, weighted = T)
 
 # get subgraphs from graph with edges of weight > min_weight
@@ -47,7 +47,11 @@ png('motif_clusters.png')
 plot(s1)
 dev.off()
 clust <- igraph::clusters(s1)
-
+if (clust$no < 1){
+  b <- lapply(files, function(f){
+    system(paste("cat",f,">",basename(f)))
+  })
+}
 # merge FASTA-files depending on the clustered graphs
 a <- lapply(seq(from = 1, to = clust$no, by = 1), function(i){
   cl <- as.vector(which(clust$membership %in% c(i)))

pipeline.nf

@@ -124,7 +124,7 @@ All arguments can be set in the configuration files
 System.exit(2)
 } else {
 	Channel.fromPath(params.bigwig).map {it -> [it.simpleName, it]}.set {bigwig_input}
-	Channel.fromPath(params.bed).set {bed_input}
+	Channel.fromPath(params.bed).into {bed_input; bed_for_tfbsscan}
 	Channel.fromPath(params.genome_fasta).into {fa_overlap; fa_scan; fa_overlap_2}
 	Channel.fromPath(params.motif_db).into {db_for_motivscan; db_for_tomtom}
 	Channel.fromPath(params.config).set {config}
@@ -205,6 +205,7 @@ process footprint_extraction {
 	"""
 }
 
+for_tfbs = fa_overlap.combine(db_for_motivscan).combine(bed_for_tfbsscan)
 
 /*
 
@@ -216,8 +217,7 @@ process extract_known_TFBS {
 	publishDir "${params.out}/known_TFBS/", mode: 'copy', pattern: '*.bed'
 
 	input:
-	file (fasta) from fa_overlap
-	file (db) from db_for_motivscan
+	set file (fasta), file (db), file (bed) from for_tfbs
 
 	output:
 	val ('done') into known_TFBS_for_overlap
@@ -227,7 +227,7 @@ process extract_known_TFBS {
 
 	script:
 	"""
-	python ${path_bin}/tfbsscan.py --use moods --core ${params.threads} -m ${db} -g ${fasta} -o ${params.create_known_tfbs_path}
+	python ${path_bin}/tfbsscan.py --use moods --core ${params.threads} -m ${db} -g ${fasta} -o ${params.create_known_tfbs_path} -b ${bed}
 	"""
 }
 
@@ -417,7 +417,7 @@ Merging FASTA-files of similar clusters
 process merge_fasta {
 	conda "${path_env}"
 	publishDir "${params.out}/esimated_motifs/merged_fasta/", mode: 'copy'
-
+	echo true
 	input:
 	set file (motiv_sim), val (fasta_list) from files_for_merge_fasta