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loosolab · Dec 15, 2018 · 50fb433 · 50fb433
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commit 50fb433
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/bin/bed_to_fasta.R b/bin/bed_to_fasta.R
@@ -14,14 +14,14 @@ min_seq <- args[3]
 
 bed <- data.table::fread(bedInput, header = FALSE, sep = "\t")
 
-clusters <- split(bed, bed$V11, sorted = TRUE, flatten = FALSE) # <---- Spalte mit Cluster
+clusters <- split(bed, bed$V11, sorted = TRUE, flatten = FALSE) # <---- Cluster column
 discard <- lapply(1:length(clusters), function(i){
   clust <- as.data.frame(clusters[i])
   print(nrow(clust))
   if (nrow(clust) >= as.numeric(min_seq) ) {
-    sequences <- as.list(clust[[10]])   # <---- Splate mit Sequenz
+    sequences <- as.list(clust[[10]])   # <---- sequenze column
     outfile <- paste0(prefix,"_cluster_",i,".FASTA")
-    seqinr::write.fasta(sequences = sequences, names = clust[[4]], file.out = outfile, as.string = TRUE) # <---- Spalte mit Name
+    seqinr::write.fasta(sequences = sequences, names = clust[[4]], file.out = outfile, as.string = TRUE) # <---- Name column
   } else {
     print(paste0("Cluster: ",i," is to small"))
   }

diff --git a/bin/motif_estimation.nf b/bin/motif_estimation.nf
@@ -24,7 +24,7 @@ motif_similarity_thresh = 0.00001 // threshold for motif similarity score
 
 if (params.bed == "" || params.out == "" || params.motif_db == "" || params.path_env || "${params.help}" == "1") {
 log.info """
-Usage: nextflow run pipeline.nf --bed [PATH] --out [PATH] --motif_db [PATH] --path_env YAML-file
+Usage: nextflow run motif_estimation.nf --bed [PATH] --out [PATH] --motif_db [PATH] --path_env YAML-file
 --bed Path			Input BED-file (Column with cluster: 11; column with sequenze: 10)!!
 --out Path			Output Path
 --motif_db Path		Path to MEME-Database