Adding report to shiva pipeline

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

 package nl.lumc.sasc.biopet.pipelines.bammetrics
 
-import java.io.{PrintWriter, File}
+import java.io.{ PrintWriter, File }
 
 import nl.lumc.sasc.biopet.core.report.{ ReportBuilder, ReportPage, ReportSection }
-import nl.lumc.sasc.biopet.core.summary.{SummaryValue, Summary}
+import nl.lumc.sasc.biopet.core.summary.{ SummaryValue, Summary }
 import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
 
 /**
@@ -65,8 +65,10 @@ object BammetricsReport extends ReportBuilder {
     }
 
     if (libraryLevel) {
-      for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
-           lib <- summary.libraries(sample)) {
+      for (
+        sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
+        lib <- summary.libraries(sample)
+      ) {
         tsvWriter.println(getLine(summary, sample, Some(lib)))
       }
     } else {
@@ -85,5 +87,4 @@ object BammetricsReport extends ReportBuilder {
     plot.runLocal()
   }
 
-
 }

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R

@@ -28,6 +28,6 @@ ggplot(DF1, aes(x = Rank, y = value, fill = variable)) +
   ylab(arguments$ylabel) + 
   guides(fill=guide_legend(title=arguments$llabel)) +
   theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
-  geom_bar(stat = "identity", width=0.75)
+  geom_bar(stat = "identity", width=1)
 
 dev.off()

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.core
 import java.io.File
 import java.io.PrintWriter
 import nl.lumc.sasc.biopet.core.config.{ ConfigValueIndex, Config, Configurable }
+import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder }
 import org.broadinstitute.gatk.utils.commandline.Argument
 import org.broadinstitute.gatk.queue.QSettings
 import org.broadinstitute.gatk.queue.function.QFunction
@@ -57,6 +58,9 @@ trait BiopetQScript extends Configurable with GatkLogging {
   /** Pipeline itself */
   def biopetScript
 
+  /** Returns the extension to make the report */
+  def reportClass: Option[ReportBuilderExtension] = None
+
   /** Script from queue itself, final to force some checks for each pipeline and write report */
   final def script() {
     outputDir = config("output_dir")
@@ -81,6 +85,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
       globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
     else BiopetQScript.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
 
+    reportClass.foreach(add(_))
+
     BiopetQScript.checkErrors
   }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -2,8 +2,9 @@ package nl.lumc.sasc.biopet.core.report
 
 import java.io.{ PrintWriter, File }
 
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.summary.Summary
+import org.broadinstitute.gatk.utils.commandline.Input
 import org.fusesource.scalate.{ TemplateSource, TemplateEngine }
 
 import scala.io.Source
@@ -11,15 +12,40 @@ import scala.io.Source
 /**
  * Created by pjvan_thof on 3/27/15.
  */
+trait ReportBuilderExtension extends BiopetJavaCommandLineFunction {
+
+  val builder: ReportBuilder
+
+  @Input(required = true)
+  var summaryFile: File = _
+
+  var outputDir: File = _
+
+  var args: Map[String, String] = Map()
+
+  override def beforeGraph: Unit = {
+    super.beforeGraph
+    jobOutputFile = new File(outputDir, ".report.log.out")
+    javaMainClass = builder.getClass.getName.takeWhile(_ != '$')
+  }
+
+  override def commandLine: String = {
+    super.commandLine +
+      required("--summary", summaryFile) +
+      required("--outputDir", outputDir) +
+      args.map(x => required(x._1, x._2)).mkString
+  }
+}
+
 trait ReportBuilder extends ToolCommand {
 
   case class Args(summary: File = null, outputDir: File = null, pageArgs: Map[String, String] = Map()) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
-    opt[File]('s', "summary") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
+    opt[File]('s', "summary") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(summary = x)
     }
-    opt[File]('o', "outputDir") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
+    opt[File]('o', "outputDir") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(outputDir = x)
     }
     opt[Map[String, String]]('a', "args") action { (x, c) =>
@@ -50,7 +76,7 @@ trait ReportBuilder extends ToolCommand {
     val cssDir = new File(cmdArgs.outputDir, "css")
     cssDir.mkdirs()
     val cssWriter = new PrintWriter(new File(cssDir, "biopet.css"))
-    Source.fromInputStream(getClass.getResourceAsStream("/nl/lumc/sasc/biopet/core/report/biopet.css")).getLines().foreach(cssWriter.println(_))
+    Source.fromInputStream(getClass.getResourceAsStream("/nl/lumc/sasc/biopet/core/report/biopet.css")).getLines().foreach(cssWriter.println)
     cssWriter.close()
 
     logger.info("Parsing summary")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala

@@ -4,7 +4,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
  * Created by pjvan_thof on 4/29/15.

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala

 package nl.lumc.sasc.biopet.pipelines.flexiprep
 
-import java.io.{PrintWriter, File}
+import java.io.{ PrintWriter, File }
 
 import nl.lumc.sasc.biopet.core.report.{ ReportSection, ReportPage, ReportBuilder }
-import nl.lumc.sasc.biopet.core.summary.{SummaryValue, Summary}
+import nl.lumc.sasc.biopet.core.summary.{ SummaryValue, Summary }
 import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
 
 /**
@@ -44,10 +44,10 @@ object FlexiprepReport extends ReportBuilder {
   // FIXME: Not yet finished
 
   def readSummaryPlot(outputDir: File,
-                         prefix: String,
-                         read: String,
-                         summary: Summary,
-                         sampleId: Option[String] = None): Unit = {
+                      prefix: String,
+                      read: String,
+                      summary: Summary,
+                      sampleId: Option[String] = None): Unit = {
     val tsvFile = new File(outputDir, prefix + ".tsv")
     val pngFile = new File(outputDir, prefix + ".png")
     val tsvWriter = new PrintWriter(tsvFile)
@@ -74,8 +74,10 @@ object FlexiprepReport extends ReportBuilder {
       sb.toString
     }
 
-    for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
-         lib <- summary.libraries(sample)) {
+    for (
+      sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
+      lib <- summary.libraries(sample)
+    ) {
       tsvWriter.println(getLine(summary, sample, lib))
     }
 
@@ -112,8 +114,10 @@ object FlexiprepReport extends ReportBuilder {
       sb.toString
     }
 
-    for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
-         lib <- summary.libraries(sample)) {
+    for (
+      sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
+      lib <- summary.libraries(sample)
+    ) {
       tsvWriter.println(getLine(summary, sample, lib))
     }
 

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import java.io.{PrintWriter, File}
+import java.io.{ PrintWriter, File }
 
-import nl.lumc.sasc.biopet.core.report.{ ReportSection, MultisampleReportBuilder, ReportPage }
-import nl.lumc.sasc.biopet.core.summary.{SummaryValue, Summary}
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, MultisampleReportBuilder, ReportPage }
+import nl.lumc.sasc.biopet.core.summary.{ SummaryValue, Summary }
 import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
 import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
@@ -11,6 +12,10 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
 /**
  * Created by pjvan_thof on 3/30/15.
  */
+class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
+  val builder = ShivaReport
+}
+
 object ShivaReport extends MultisampleReportBuilder {
 
   // FIXME: Not yet finished
@@ -74,10 +79,10 @@ object ShivaReport extends MultisampleReportBuilder {
   def reportName = "Shiva Report"
 
   def variantSummaryPlot(outputDir: File,
-                           prefix: String,
-                           summary: Summary,
-                           libraryLevel: Boolean = false,
-                           sampleId: Option[String] = None): Unit = {
+                         prefix: String,
+                         summary: Summary,
+                         libraryLevel: Boolean = false,
+                         sampleId: Option[String] = None): Unit = {
     val tsvFile = new File(outputDir, prefix + ".tsv")
     val pngFile = new File(outputDir, prefix + ".png")
     val tsvWriter = new PrintWriter(tsvFile)
@@ -103,8 +108,10 @@ object ShivaReport extends MultisampleReportBuilder {
     }
 
     if (libraryLevel) {
-      for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
-           lib <- summary.libraries(sample)) {
+      for (
+        sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
+        lib <- summary.libraries(sample)
+      ) {
         tsvWriter.println(getLine(summary, sample, Some(lib)))
       }
     } else {

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

@@ -45,6 +45,13 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
     addSummaryJobs
   }
 
+  override def reportClass = {
+    val shiva = new ShivaReport(this)
+    shiva.outputDir = new File(outputDir, "report")
+    shiva.summaryFile = summaryFile
+    Some(shiva)
+  }
+
   /** Method to make the variantcalling submodule of shiva */
   def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait = {
     if (multisample) new ShivaVariantcalling(qscript) {