Commit ff74a677 authored by bow's avatar bow
Browse files

Update main executable pipelines and tool visibility

parent 47b5dd69
......@@ -7,8 +7,6 @@ package nl.lumc.sasc.biopet.core
object BiopetExecutableProtected extends BiopetExecutable {
def pipelines: List[MainCommand] = BiopetExecutablePublic.protectedPipelines ::: List(
nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling,
nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline,
nl.lumc.sasc.biopet.pipelines.gatk.Shiva,
nl.lumc.sasc.biopet.pipelines.gatk.ShivaVariantcalling,
nl.lumc.sasc.biopet.pipelines.gatk.Basty)
......
......@@ -21,10 +21,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.mapping.Mapping,
nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap,
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics,
nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp,
nl.lumc.sasc.biopet.pipelines.sage.Sage,
nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig,
nl.lumc.sasc.biopet.pipelines.kopisu.ConiferPipeline,
nl.lumc.sasc.biopet.pipelines.carp.Carp,
nl.lumc.sasc.biopet.pipelines.toucan.Toucan
)
......@@ -46,7 +44,6 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl.lumc.sasc.biopet.tools.VcfFilter,
nl.lumc.sasc.biopet.tools.VcfStats,
nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
nl.lumc.sasc.biopet.tools.BedToInterval,
nl.lumc.sasc.biopet.tools.MpileupToVcf,
nl.lumc.sasc.biopet.tools.FastqSplitter,
nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
......
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