From dd813f33ad81bae5154ff01d763f8a7e40e075a0 Mon Sep 17 00:00:00 2001 From: Peter van 't Hof Date: Thu, 9 Mar 2017 16:09:09 +0100 Subject: [PATCH] Fix format --- .../nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 61037de4b..cf73c31a0 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") -- GitLab