Commit 6ac2ce38 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added reference to bamMetrics

parent 25d38d41
......@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.{ Reference, BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
import nl.lumc.sasc.biopet.extensions.picard._
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
......@@ -27,7 +27,11 @@ import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import org.broadinstitute.gatk.queue.QScript
class BamMetrics(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
class BamMetrics(val root: Configurable) extends QScript
with SummaryQScript
with SampleLibraryTag
with Reference {
def this() = this(null)
@Input(doc = "Bam File", shortName = "BAM", required = true)
......@@ -51,7 +55,8 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
}
/** returns files to store in summary */
def summaryFiles = Map("input_bam" -> inputBam) ++
def summaryFiles = Map("reference" -> referenceFasta(),
"input_bam" -> inputBam) ++
ampliconBedFile.map("amplicon" -> _).toMap ++
ampliconBedFile.map(x => "roi_" + x.getName.stripSuffix(".bed") -> x).toMap
......
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