Commit 76381e8c authored by Peter van 't Hof's avatar Peter van 't Hof

Remove protected executable

parent e19b18ba
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet
import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
object BiopetExecutableProtected extends BiopetExecutable {
def pipelines: List[MainCommand] = BiopetExecutablePublic.publicPipelines ::: List(
nl.lumc.sasc.biopet.pipelines.gatk.Shiva)
def tools = BiopetExecutablePublic.tools
}
\ No newline at end of file
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet
import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
object BiopetExecutablePublic extends BiopetExecutable {
def publicPipelines: List[MainCommand] = List(
def pipelines: List[MainCommand] = List(
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep,
nl.lumc.sasc.biopet.pipelines.mapping.Mapping,
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMapping,
......@@ -34,12 +34,9 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.gears.Gears,
nl.lumc.sasc.biopet.pipelines.gwastest.GwasTest,
nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
nl.lumc.sasc.biopet.pipelines.basty.Basty
)
def pipelines: List[MainCommand] = List(
nl.lumc.sasc.biopet.pipelines.basty.Basty,
nl.lumc.sasc.biopet.pipelines.shiva.Shiva
) ::: publicPipelines
)
def tools: List[MainCommand] = BiopetToolsExecutable.tools
}
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