Commit b83e9b26 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing output file

parent b32296d9
......@@ -87,7 +87,10 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String)
require(read != null)
deps ::= input
outputFiles :+= output
trim.foreach(outputFiles :+= _.outputStats)
trim.foreach { t =>
t.outputStats = new File(output.getParentFile, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.trim.stats")
outputFiles :+= t.outputStats
}
}
override def beforeCmd(): Unit = {
......@@ -134,8 +137,6 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String)
case Some(c) => c.fastqOutput
case _ => seqtk.output
}
t.outputStats = new File(output.getParentFile, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.trim.stats")
outputFiles :+= t.outputStats
addPipeJob(t)
}
......
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