Commit 849188d8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix default aligner in constructor

parent 71b12276
......@@ -287,7 +287,7 @@ object Mapping extends PipelineCommand {
var inputType = ""
if (runConfig.contains("inputtype")) inputType = runConfig("inputtype").toString
else inputType = root.config("inputtype", "dna").getString
if (inputType == "rna") mapping.aligner = root.config("rna_aligner", "star-2pass").getString
if (inputType == "rna") mapping.defaultAligner = "star-2pass"
if (runConfig.contains("R1")) mapping.input_R1 = new File(runConfig("R1").toString)
if (runConfig.contains("R2")) mapping.input_R2 = new File(runConfig("R2").toString)
mapping.paired = (mapping.input_R2 != null)
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