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Commit 02b6241f authored by Peter van 't Hof's avatar Peter van 't Hof
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Merge branch 'refactor_core-funcs' into 'master' 

Refactor core funcs
parents fcaccd90 4e14ca72
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with 19 additions and 18 deletions
biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
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− 1
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/*
/*
* Copyright (c) 2012 The Broad Institute
* Modifications (c) 2014 Leiden University Medical Center
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
......
biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala
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package nl.lumc.sasc.biopet.wrappers
package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.InProcessFunction
......
biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Python.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Python.scala
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package nl.lumc.sasc.biopet.wrappers
package nl.lumc.sasc.biopet.function
import java.io.FileOutputStream
import nl.lumc.sasc.biopet.core._
......
biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
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package nl.lumc.sasc.biopet.wrappers
package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
......
biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
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package nl.lumc.sasc.biopet.wrappers
package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
......
flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
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package nl.lumc.sasc.biopet.wrappers.fastq
package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
......
flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
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package nl.lumc.sasc.biopet.wrappers.fastq
package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
......
flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
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package nl.lumc.sasc.biopet.wrappers.fastq
package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
......
flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
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− 2
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package nl.lumc.sasc.biopet.pipelines.flexiprep
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.wrappers._
import nl.lumc.sasc.biopet.wrappers.fastq._
import nl.lumc.sasc.biopet.function._
import nl.lumc.sasc.biopet.function.fastq._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard._
......
flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
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......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
//import java.io.FileOutputStream
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.wrappers._
import nl.lumc.sasc.biopet.function._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
......
flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
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− 1
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......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import nl.lumc.sasc.biopet.wrappers.Python
import nl.lumc.sasc.biopet.function.Python
import org.broadinstitute.sting.commandline._
import java.io.File
......
flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
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......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import nl.lumc.sasc.biopet.wrappers.Python
import nl.lumc.sasc.biopet.function.Python
import org.broadinstitute.sting.commandline._
import java.io.File
......
flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
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......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import nl.lumc.sasc.biopet.wrappers.Python
import nl.lumc.sasc.biopet.function.Python
import org.broadinstitute.sting.commandline._
import java.io.File
......
flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
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......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import nl.lumc.sasc.biopet.wrappers.Python
import nl.lumc.sasc.biopet.function.Python
import org.broadinstitute.sting.commandline._
import java.io.File
......
gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala → gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
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package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.wrappers._
import nl.lumc.sasc.biopet.wrappers.aligners._
import nl.lumc.sasc.biopet.function._
import nl.lumc.sasc.biopet.function.aligners._
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.pipelines.mapping._
import nl.lumc.sasc.biopet.pipelines.flexiprep._
......
mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala → mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala
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package nl.lumc.sasc.biopet.wrappers.aligners
package nl.lumc.sasc.biopet.function.aligners
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
......
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