Commit cf5683e9 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed outputFiles of fifo pipe

parent 7c8fe6be
......@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.core
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.Output
/**
* Created by pjvan_thof on 9/29/15.
......@@ -46,6 +47,9 @@ class BiopetFifoPipe(val root: Configurable,
) yield outputFile
}
@Output
private var outputFiles: List[File] = Nil
override def beforeGraph(): Unit = {
val outputs: Map[BiopetCommandLineFunction, Seq[File]] = try {
commands.map(x => x -> x.outputs).toMap
......@@ -61,6 +65,9 @@ class BiopetFifoPipe(val root: Configurable,
val fifoFiles = fifos
outputFiles :::= outputs.values.toList.flatten.filter(!fifoFiles.contains(_))
outputFiles = outputFiles.distinct
deps :::= inputs.values.toList.flatten.filter(!fifoFiles.contains(_))
deps = deps.distinct
......
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