diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala index 61037de4b52ba3d60609f68132d8c89d88b3eed4..cf73c31a040833003771c5c22db1908591386a53 100644 --- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala +++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala @@ -123,7 +123,7 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String) Some(cutadapt) } else None case (None, _) => None - case (Some(c), _) => + case (Some(c), _) => c.fastqInput = seqtk.output c.fastqOutput = new File(output.getParentFile, input.getName + ".cutadapt.fq") c.statsOutput = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")