Merge pull request #10 from biopet/fix-BIOPET-534

Fix biopet 534

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

@@ -19,7 +19,6 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, WriteSummary }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
-import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
 import nl.lumc.sasc.biopet.utils.Logging
 import org.broadinstitute.gatk.queue.{ QScript, QSettings }
 import org.broadinstitute.gatk.queue.function.QFunction
@@ -118,11 +117,10 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
     }
 
     functions.filter(_.jobOutputFile == null).foreach(f => {
-      try {
-        val className = if (f.getClass.isAnonymousClass) f.getClass.getSuperclass.getSimpleName else f.getClass.getSimpleName
-        f.jobOutputFile = new File(f.firstOutput.getAbsoluteFile.getParent, "." + f.firstOutput.getName + "." + className + ".out")
-      } catch {
-        case e: NullPointerException => logger.warn(s"Can't generate a jobOutputFile for $f")
+      val className = if (f.getClass.isAnonymousClass) f.getClass.getSuperclass.getSimpleName else f.getClass.getSimpleName
+      BiopetQScript.safeOutputs(f) match {
+        case Some(o) => f.jobOutputFile = new File(o.head.getAbsoluteFile.getParent, "." + f.firstOutput.getName + "." + className + ".out")
+        case _ => f.jobOutputFile = new File("./stdout") // Line is here for test backup
       }
     })
 
@@ -159,7 +157,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       case that: BiopetQScript =>
         that.init()
         that.biopetScript()
-      case _ => subPipeline.script
+      case _ => subPipeline.script()
     }
     addAll(subPipeline.functions)
   }

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala

@@ -101,6 +101,9 @@ object WriteDependencies extends Logging with Configurable {
         file.addOutputJob(function)
         files += output -> file
       }
+      val file = files.getOrElse(function.jobOutputFile, QueueFile(function.jobOutputFile))
+      file.addOutputJob(function)
+      files += function.jobOutputFile -> file
     }
 
     val jobs = functionNames.par.map {
@@ -116,7 +119,7 @@ object WriteDependencies extends Logging with Configurable {
           "depends_on_intermediate" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).exists(files(_).isIntermediate),
           "depends_on_jobs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList.flatMap(files(_).outputJobNames).distinct,
           "output_used_by_jobs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList.flatMap(files(_).inputJobNames).distinct,
-          "outputs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList,
+          "outputs" -> (f.jobOutputFile :: BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList),
           "inputs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList,
           "done_files" -> BiopetQScript.safeDoneFiles(f).getOrElse(Seq()).toList,
           "fail_files" -> BiopetQScript.safeFailFiles(f).getOrElse(Seq()).toList,

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

@@ -40,10 +40,10 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   var vepScript: String = config("vep_script")
 
   @Input(doc = "input VCF", required = true)
-  var input: File = null
+  var input: File = _
 
   @Output(doc = "output file", required = true)
-  var output: File = null
+  var output: File = _
 
   override def subPath = {
     if (vepVersion.isSet) super.subPath ++ List("vep_settings") ++ vepVersion()
@@ -160,7 +160,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   override def defaultCoreMemory = 4.0
 
   @Output
-  private var _summary: File = null
+  private var _summary: File = _
 
   override def beforeGraph(): Unit = {
     super.beforeGraph()
@@ -312,11 +312,11 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
 
     (for ((header, headerIndex) <- headers) yield {
       val name = header.stripPrefix("[").stripSuffix("]")
-      name.replaceAll(" ", "_") -> (contents.drop(headerIndex + 1).takeWhile(!isHeader(_)).flatMap { line =>
+      name.replaceAll(" ", "_") -> contents.drop(headerIndex + 1).takeWhile(!isHeader(_)).flatMap { line =>
         val values = line.split("\t", 2)
         if (values.last.isEmpty || values.last == "-") None
         else Some(values.head.replaceAll(" ", "_") -> tryToParseNumber(values.last).getOrElse(values.last))
-      }.toMap)
+      }.toMap
     }).toMap
   }
 }

biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/UtilsTest.scala

@@ -6,6 +6,7 @@ import org.testng.annotations.Test
 
 /**
  * Created by Sander Bollen on 12-10-16.
+ * Here we test utils
  */
 class UtilsTest extends TestNGSuite with Matchers {
 

biopet-utils/src/test/scala/VcfUtilsTest.scala → biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/VcfUtilsTest.scala

-import htsjdk.variant.variantcontext.{ Allele, Genotype, GenotypeBuilder }
+package nl.lumc.sasc.biopet.utils
+
+import htsjdk.variant.variantcontext.{ Allele, GenotypeBuilder }
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
 import scala.collection.JavaConversions._
 
-import nl.lumc.sasc.biopet.utils.VcfUtils
-
 /**
  * Created by Sander Bollen on 4-10-16.
  */

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala

@@ -50,7 +50,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
     val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
     val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
     val insertsizeExecuted = summary.getSampleValues("bammetrics", "stats", "CollectInsertSizeMetrics", "metrics").values.exists(_ != Some(None))
-    val mappingExecuted = summary.getLibraryValues("mapping").nonEmpty
+    val mappingExecuted = summary.getLibraryValues("mapping").exists(_._2.isDefined)
     val pairedFound = !mappingExecuted || summary.getLibraryValues("mapping", "settings", "paired").exists(_._2 == Some(true))
     val flexiprepExecuted = summary.getLibraryValues("flexiprep")
       .exists { case ((sample, lib), value) => value.isDefined }