Commit 206c7f01 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix fastqc dependency

parent 7a3bf3b2
...@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep ...@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetPipe } import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetPipe }
import nl.lumc.sasc.biopet.extensions.{Cat, Gzip, Sickle, Cutadapt} import nl.lumc.sasc.biopet.extensions.{ Cat, Gzip, Sickle, Cutadapt }
import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input } import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
...@@ -31,7 +31,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman ...@@ -31,7 +31,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
override def beforeGraph(): Unit = { override def beforeGraph(): Unit = {
super.beforeGraph() super.beforeGraph()
require(read != null) require(read != null)
deps :::= fastqc.outputFiles deps ::= output
} }
override def defaultCoreMemory = 2.0 override def defaultCoreMemory = 2.0
......
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