Added wgs metrics

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

@@ -72,6 +72,11 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
 
     add(CollectGcBiasMetrics(this, inputBam, outputDir))
 
+    val wgsMetrics = new CollectWgsMetrics(this)
+    wgsMetrics.input = inputBam
+    wgsMetrics.output = swapExt(outputDir, inputBam, ".bam", ".rna.metrics")
+    add(wgsMetrics)
+
     if (rnaMetrics) {
       val rnaMetrics = new CollectRnaSeqMetrics(this)
       rnaMetrics.input = inputBam
@@ -135,7 +140,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
       val coverageFile = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
 
       //FIXME:should use piping
-      add(BedtoolsCoverage(this, inputBam, intervals.bed, coverageFile, depth = true), isIntermediate = true)
+      add(BedtoolsCoverage(this, inputBam, intervals.bed, coverageFile, depth = true), true)
       add(CoverageStats(this, coverageFile, targetDir))
     }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala

@@ -61,8 +61,8 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard {
   override def commandLine = super.commandLine +
     required("INPUT=", input, spaceSeparated = false) +
     required("OUTPUT=", outputName, spaceSeparated = false) +
-    required("ASSUME_SORTED=", assumeSorted, spaceSeparated = false) +
-    required("STOP_AFTER=", stopAfter, spaceSeparated = false) +
+    conditional(assumeSorted, "ASSUME_SORTED=true") +
+    optional("STOP_AFTER=", stopAfter, spaceSeparated = false) +
     repeat("PROGRAM=", program, spaceSeparated = false)
 }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.picard
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output, Input }
 
 /**
  * Created by pjvan_thof on 4/16/15.

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala

+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output, Input }
+
+/**
+ * Created by pjvan_thof on 4/16/15.
+ */
+class CollectWgsMetrics(val root: Configurable) extends Picard {
+
+  javaMainClass = new picard.analysis.CollectWgsMetrics().getClass.getName
+
+  @Input(doc = "The input SAM or BAM files to analyze", required = true)
+  var input: File = null
+
+  @Output(doc = "Metrics file", required = true)
+  var output: File = null
+
+  @Input(doc = "Reference", required = true)
+  var reference: File = config("reference")
+
+  @Argument(doc = "MINIMUM_MAPPING_QUALITY", required = false)
+  var minMapQ: Option[Int] = config("minimum_mapping_quality")
+
+  @Argument(doc = "MINIMUM_BASE_QUALITY", required = false)
+  var minBaseQ: Option[Int] = config("minimum_base_quality")
+
+  @Argument(doc = "COVERAGE_CAP", required = false)
+  var covCap: Option[Int] = config("coverage_cap")
+
+  @Argument(doc = "STOP_AFTER", required = false)
+  var stopAfter: Option[Long] = config("stop_after")
+
+  @Argument(doc = "INCLUDE_BQ_HISTOGRAM", required = false)
+  var includeBqHistogram: Boolean = config("include_bq_histogram", default = false)
+
+  override def commandLine = super.commandLine +
+    required("INPUT=", input, spaceSeparated = false) +
+    required("OUTPUT=", output, spaceSeparated = false) +
+    required("REFERENCE_SEQUENCE=", reference, spaceSeparated = false) +
+    optional("MINIMUM_MAPPING_QUALITY=", minMapQ, spaceSeparated = false) +
+    optional("MINIMUM_BASE_QUALITY=", minBaseQ, spaceSeparated = false) +
+    optional("COVERAGE_CAP=", covCap, spaceSeparated = false) +
+    optional("STOP_AFTER=", stopAfter, spaceSeparated = false) +
+    conditional(includeBqHistogram, "INCLUDE_BQ_HISTOGRAM=true")
+}