Commit 86e140da authored by Lena Hersemann's avatar Lena Hersemann

removed empty default for --out (files prefix)

parent 351a906d
......@@ -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)
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