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Commit 6f44aea3 authored by Peter van 't Hof's avatar Peter van 't Hof
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Moved Sage tools to nl.lumc.biopet.tools

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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
+ 3
− 3
View file @ 6f44aea3
...@@ -30,9 +30,9 @@ object BiopetExecutable { ...@@ -30,9 +30,9 @@ object BiopetExecutable {
nl.lumc.sasc.biopet.tools.MpileupToVcf, nl.lumc.sasc.biopet.tools.MpileupToVcf,
nl.lumc.sasc.biopet.tools.FastqSplitter, nl.lumc.sasc.biopet.tools.FastqSplitter,
nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts, nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
nl.lumc.sasc.biopet.pipelines.sage.SageCountFastq, nl.lumc.sasc.biopet.tools.SageCountFastq,
nl.lumc.sasc.biopet.pipelines.sage.SageCreateLibrary, nl.lumc.sasc.biopet.tools.SageCreateLibrary,
nl.lumc.sasc.biopet.pipelines.sage.SageCreateTagCounts) nl.lumc.sasc.biopet.tools.SageCreateTagCounts)
) )
/** /**
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+ 3
− 0
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...@@ -10,6 +10,9 @@ import nl.lumc.sasc.biopet.pipelines.mapping.Mapping ...@@ -10,6 +10,9 @@ import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import nl.lumc.sasc.biopet.scripts.PrefixFastq import nl.lumc.sasc.biopet.scripts.PrefixFastq
import nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts import nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts
import nl.lumc.sasc.biopet.scripts.SquishBed import nl.lumc.sasc.biopet.scripts.SquishBed
import nl.lumc.sasc.biopet.tools.SageCountFastq
import nl.lumc.sasc.biopet.tools.SageCreateLibrary
import nl.lumc.sasc.biopet.tools.SageCreateTagCounts
import org.broadinstitute.gatk.queue.QScript import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.function._ import org.broadinstitute.gatk.queue.function._
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/SageCountFastq.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
+ 1
− 1
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package nl.lumc.sasc.biopet.pipelines.sage package nl.lumc.sasc.biopet.tools
import java.io.File import java.io.File
import java.io.PrintWriter import java.io.PrintWriter
......
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/SageCreateLibrary.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
+ 1
− 1
View file @ 6f44aea3
package nl.lumc.sasc.biopet.pipelines.sage package nl.lumc.sasc.biopet.tools
import java.io.File import java.io.File
import java.io.PrintWriter import java.io.PrintWriter
......
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/SageCreateTagCounts.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
+ 1
− 1
View file @ 6f44aea3
package nl.lumc.sasc.biopet.pipelines.sage package nl.lumc.sasc.biopet.tools
import java.io.File import java.io.File
import java.io.PrintWriter import java.io.PrintWriter
......
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