From 6ac2ce38abeee9bc19436c43613975a3bdbe4faf Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 29 Oct 2015 15:02:49 +0100
Subject: [PATCH] Added reference to bamMetrics
---
.../sasc/biopet/pipelines/bammetrics/BamMetrics.scala | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index 981417a01..f0c947860 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -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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