Commit 8c5573ad authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge pull request #71 from biopet/fix-BIOPET-651

Adding a adapter cutoff for fastqc -> cutadapt
parents 865f33cf 5e121141
......@@ -206,7 +206,9 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
val foundAdapters = modules.get("Adapter Content").map { x =>
val header = x.lines.head.split("\t").tail.zipWithIndex
val lines = x.lines.tail.map(_.split("\t").tail)
val found = header.filter(h => lines.exists(x => x(h._2).toFloat > 0)).map(_._1)
val found = header
.filter(h => lines.exists(x => x(h._2).toFloat > adapterCutoff))
.map(_._1)
adapterSet.filter(x => found.contains(x.name))
}
......@@ -214,6 +216,8 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
} else Set()
}
val adapterCutoff: Float = config("adapter_cutoff", default = 0.001)
@Output
private var outputFiles: List[File] = Nil
......
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