Commit b86d33ee authored by Peter van 't Hof's avatar Peter van 't Hof

Move input files back to beforeGraph

parent b9b1a0b0
......@@ -49,10 +49,6 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc, val read: String) ex
var trim: Option[Sickle] = if (!flexiprep.skipTrim) {
val sickle = new Sickle(root)
sickle.outputStats = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.trim.stats")
sickle.inputR1 = clip match {
case Some(c) => c.fastqOutput
case _ => seqtk.output
}
Some(sickle)
} else None
......@@ -130,6 +126,10 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc, val read: String) ex
trim.foreach { t =>
t.outputR1 = new File(output.getParentFile, input.getName + ".sickle.fq")
t.inputR1 = clip match {
case Some(c) => c.fastqOutput
case _ => seqtk.output
}
addPipeJob(t)
}
......
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