Added summaries

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -9,6 +9,7 @@ import nl.lumc.sasc.biopet.core.MultiSampleQScript
 import nl.lumc.sasc.biopet.core.PipelineCommand
 import nl.lumc.sasc.biopet.core.config.Configurable
 import htsjdk.samtools.SamReaderFactory
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import scala.collection.JavaConversions._
 import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, CombineGVCFs }
@@ -19,7 +20,7 @@ import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.utils.commandline.{ Argument }
 
-class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScript {
+class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScript with SummaryQScript {
   qscript =>
   def this() = this(null)
 
@@ -40,6 +41,12 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   var useAllelesOption: Boolean = config("use_alleles_option", default = false)
   val externalGvcfs = config("external_gvcfs_files", default = Nil).asFileList
 
+  def summaryFile = new File(outputDir, "GatkPipeline.summary.json")
+
+  def summaryFiles = Map()
+
+  def summaryData = Map()
+
   def makeSample(id: String) = new Sample(id)
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
     def makeLibrary(id: String) = new Library(id)
@@ -118,13 +125,15 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
           gatkVariantcalling.biopetScript
           addAll(gatkVariantcalling.functions)
         }
+
+        addSummaryQScript(mapping)
       }
     }
 
     /** sample variantcalling */
     val gatkVariantcalling = new GatkVariantcalling(qscript)
     gatkVariantcalling.sampleID = sampleId
-    gatkVariantcalling.outputDir = new File(sampleDir, "variantcalling/")
+    gatkVariantcalling.outputDir = new File(sampleDir, "variantcalling")
 
     protected def addJobs(): Unit = {
       addPerLibJobs()
@@ -152,6 +161,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
 
   def biopetScript(): Unit = {
     addSamplesJobs()
+
+    addSummaryJobs
   }
 
   def addMultiSampleJobs(): Unit = {

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -15,9 +15,10 @@
  */
 package nl.lumc.sasc.biopet.pipelines.bammetrics
 
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.scripts.CoverageStats
 import org.broadinstitute.gatk.queue.QScript
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.core.{ SampleLibraryTag, BiopetQScript, PipelineCommand }
 import java.io.File
 import nl.lumc.sasc.biopet.tools.{ BedToInterval, BiopetFlagstat }
 import nl.lumc.sasc.biopet.core.config.Configurable
@@ -25,7 +26,7 @@ import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsInter
 import nl.lumc.sasc.biopet.extensions.picard.{ CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics, CollectAlignmentSummaryMetrics }
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
 
-class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
+class BamMetrics(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
   def this() = this(null)
 
   @Input(doc = "Bam File", shortName = "BAM", required = true)
@@ -40,6 +41,16 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
   @Argument(doc = "", required = false)
   var wholeGenome = false
 
+  def summaryFile = (sampleId, libId) match {
+    case (Some(sampleId), Some(libId)) => new File(outputDir, sampleId + "-" + libId + ".BamMetrics.summary.json")
+    case (Some(sampleId), _)           => new File(outputDir, sampleId + ".BamMetrics.summary.json")
+    case _                             => new File(outputDir, "BamMetrics.summary.json")
+  }
+
+  def summaryFiles = Map("input_bam" -> inputBam)
+
+  def summaryData = Map()
+
   def init() {
     if (config.contains("target_bed")) {
       for (file <- config("target_bed").asList) {
@@ -81,6 +92,8 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
       add(BedtoolsCoverage(this, inputBam, bedFile, coverageFile, true), true)
       add(CoverageStats(this, coverageFile, targetDir))
     }
+
+    addSummaryJobs
   }
 }
 

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -215,7 +215,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
       bamFile = mergeSamFile.output
     }
 
-    if (!skipMetrics) addAll(BamMetrics(this, bamFile, new File(outputDir, "metrics")).functions)
+    if (!skipMetrics) {
+      val bamMetrics = BamMetrics(this, bamFile, new File(outputDir, "metrics"))
+      addAll(bamMetrics.functions)
+      addSummaryQScript(bamMetrics)
+    }
 
     add(Ln(this, swapExt(outputDir, bamFile, ".bam", ".bai"), swapExt(outputDir, finalBamFile, ".bam", ".bai")))
     add(Ln(this, bamFile, finalBamFile))