Fixing BIOPET-491

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala

@@ -42,4 +42,6 @@ trait Summarizable {
   def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
     throw new IllegalStateException("Merge can not have same key by default")
   }
+
+  def summaryDeps: List[File] = Nil
 }

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -56,13 +56,16 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
   def init(): Unit = {
     for (q <- qscript.summaryQScripts)
       deps :+= q.summaryFile
-    for ((_, l) <- qscript.summarizables; s <- l) s match {
-      case f: QFunction if qscript.functions.contains(f) => try {
-        deps :+= f.firstOutput
-      } catch {
-        case e: NullPointerException => logger.warn("Queue values are not init")
+    for ((_, l) <- qscript.summarizables; s <- l) {
+      deps :::= s.summaryDeps
+      s match {
+        case f: QFunction if qscript.functions.contains(f) => try {
+          deps :+= f.firstOutput
+        } catch {
+          case e: NullPointerException => logger.warn("Queue values are not init")
+        }
+        case _ =>
       }
-      case _ =>
     }
 
     jobOutputFile = new File(out.getParentFile, ".%s.%s.out".format(out.getName, analysisName))

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

@@ -84,6 +84,8 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
       (if (outputAsStsout) "" else " > " + required(outputStats))
   }
 
+  override def summaryDeps = outputStats :: super.summaryDeps
+
   /** returns stats map for summary */
   def summaryStats: Map[String, Any] = {
     // regex for single run

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala

@@ -94,6 +94,8 @@ class FastqSync(val root: Configurable) extends ToolCommandFunction with Summari
     )
   }
 
+  override def summaryDeps = outputStats :: super.summaryDeps
+
   override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
     (v1, v2) match {
       case (v1: Int, v2: Int) => v1 + v2

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -14,12 +14,12 @@
  */
 package nl.lumc.sasc.biopet.pipelines.flexiprep
 
-import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat }
+import nl.lumc.sasc.biopet.core.summary.{Summarizable, SummaryQScript}
+import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, PipelineCommand, SampleLibraryTag}
+import nl.lumc.sasc.biopet.extensions.{Gzip, Zcat}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.IoUtils._
-import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, SeqStat, ValidateFastq }
+import nl.lumc.sasc.biopet.extensions.tools.{FastqSync, SeqStat, ValidateFastq}
 import nl.lumc.sasc.biopet.utils.Logging
 import org.broadinstitute.gatk.queue.QScript
 
@@ -206,8 +206,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
       fqSync.outputFastq2 = new File(outDir, fastqR2Qc.get.getName)
       fqSync.outputStats = new File(outDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.sync.stats")
 
-      val pipe = new BiopetFifoPipe(this, fqSync :: Nil) {
-        override def configNamespace = "qc-cmd"
+      val pipe = new BiopetFifoPipe(this, fqSync :: Nil) with Summarizable {
+        override def configNamespace = "qc_cmd"
 
         override def beforeGraph(): Unit = {
           fqSync.beforeGraph()
@@ -223,11 +223,20 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
           commands.foreach(addPipeJob)
           super.beforeCmd()
         }
+
+        /** Must return files to store into summary */
+        def summaryFiles: Map[String, File] = Map()
+
+        /** Must returns stats to store into summary */
+        def summaryStats: Any = Map()
+
+        override def summaryDeps = qcCmdR1.summaryDeps ::: qcCmdR2.summaryDeps ::: super.summaryDeps
       }
 
       pipe.deps ::= fastqcR1.output
       pipe.deps ::= fastqcR2.output
       pipe.isIntermediate = !keepQcFastqFiles
+      addSummarizable(pipe, "qc_cmd")
       add(pipe)
 
       addSummarizable(fqSync, "fastq_sync")

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala

@@ -65,6 +65,8 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
 
   def summaryStats = Map()
 
+  override def summaryDeps = trim.map(_.summaryDeps).toList.flatten ::: super.summaryDeps
+
   override def addToQscriptSummary(qscript: SummaryQScript, name: String): Unit = {
     clip match {
       case Some(job) => qscript.addSummarizable(job, s"clipping_$read")