removed empty default for --out (files prefix)

dge_workflow/featcounts_deseq_mf.R

@@ -35,7 +35,7 @@ Options:
 --qcutoff <qcutoff>             Use a q-value cutoff of 0.01 instead of a q-value cutoff [default: 0.01]
 --pcutoff <pcutoff>             Override q-value filter and filter by p-value instead
 --min_count <min_count>         Minimal expression in any of the sample to be included in the final result list [default: 10]
---out <name_prefix>             Name to prefix all generated result files [default: ]
+--out <name_prefix>             Name to prefix all generated result files
 --design <formula>              Design fomula for DeSeq with contrast attribute at the end [default: condition]
 --lfc <lfc_cutoff>              Just report genes with abs(lfc) > lfc_cutoff as hits [default: 1.0]
 --ensembl_db <ensembl_db>       Ensebmbl db to be used. If not specified inferred from data. TODO implement NONE here!!
@@ -75,7 +75,7 @@ sub_data = as.logical(opts$sub_data)
 gene_info_file = opts$gene_info
 assert(is.null(gene_info_file) || file.exists(gene_info_file), "invalid gene_info_file")
 
-resultsBase = if (str_length(opts$out) > 0) paste0(opts$out, ".") else ""
+resultsBase = if (!is.null(opts$out)) paste0(opts$out, ".") else ""
 
 pcutoff = if (is.null(opts$pcutoff))NULL else as.numeric(opts$pcutoff)
 qcutoff = if (is.numeric(pcutoff))NULL else as.numeric(opts$qcutoff)