Commit 3c73be57 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change from error to warning

parent 86ecb782
...@@ -153,8 +153,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S ...@@ -153,8 +153,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
require(inputR1 != null, "Missing inputR1 on mapping module") require(inputR1 != null, "Missing inputR1 on mapping module")
require(sampleId.isDefined, "Missing sample ID on mapping module") require(sampleId.isDefined, "Missing sample ID on mapping module")
require(libId.isDefined, "Missing library ID on mapping module") require(libId.isDefined, "Missing library ID on mapping module")
if (inputR1.exists() && inputR1.length() == 0) Logging.addError(s"Input R1 is a empty file: $inputR1") if (inputR1.exists() && inputR1.length() == 0) logger.warn(s"Input R1 is a empty file: $inputR1")
inputR2.foreach(r => if (r.exists() && r.length() == 0) Logging.addError(s"Input R2 is a empty file: $r")) inputR2.foreach(r => if (r.exists() && r.length() == 0) logger.warn(s"Input R2 is a empty file: $r"))
inputFiles :+= new InputFile(inputR1) inputFiles :+= new InputFile(inputR1)
inputR2.foreach(inputFiles :+= new InputFile(_)) inputR2.foreach(inputFiles :+= new InputFile(_))
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