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biopet.biopet
Commit dd813f33 authored by Peter van 't Hof's avatar Peter van 't Hof
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Fix format

parent 02b8fdad
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @ dd813f33
...@@ -123,7 +123,7 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String) ...@@ -123,7 +123,7 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String)
Some(cutadapt) Some(cutadapt)
} else None } else None
case (None, _) => None case (None, _) => None
case (Some(c), _) => case (Some(c), _) =>
c.fastqInput = seqtk.output c.fastqInput = seqtk.output
c.fastqOutput = new File(output.getParentFile, input.getName + ".cutadapt.fq") 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")}.$read.clip.stats") c.statsOutput = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")
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