Rename data to settings

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

@@ -45,7 +45,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
 
   def summaryFiles = Map()
 
-  def summaryData = Map()
+  def summarySettings = Map()
 
   def makeSample(id: String) = new Sample(id)
   class Sample(sampleId: String) extends AbstractSample(sampleId) {

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

@@ -49,7 +49,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
 
   def summaryFiles = Map("input_bam" -> inputBam)
 
-  def summaryData = Map()
+  def summarySettings = Map()
 
   def init() {
     if (config.contains("target_bed")) {

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

@@ -2,13 +2,15 @@ package nl.lumc.sasc.biopet.core.summary
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{ SampleLibraryTag, BiopetQScript }
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunctionTrait, BiopetCommandLineFunction, SampleLibraryTag, BiopetQScript }
 import nl.lumc.sasc.biopet.extensions.Md5sum
 
+import scala.collection.mutable
+
 /**
  * Created by pjvan_thof on 2/14/15.
  */
-trait SummaryQScript extends BiopetQScript with Summarizable {
+trait SummaryQScript extends BiopetQScript {
 
   /** Key is sample/library, None is sample or library is not applicable */
   private[summary] var summarizables: Map[(String, Option[String], Option[String]), List[Summarizable]] = Map()
@@ -16,6 +18,10 @@ trait SummaryQScript extends BiopetQScript with Summarizable {
 
   var summaryName = configName
 
+  def summarySettings: Map[String, Any]
+
+  def summaryFiles: Map[String, File]
+
   def summaryFile: File
 
   def addSummarizable(summarizable: Summarizable, name: String): Unit = {
@@ -41,10 +47,7 @@ trait SummaryQScript extends BiopetQScript with Summarizable {
   def addSummaryJobs: Unit = {
     val writeSummary = new WriteSummary(this)
 
-    addSummarizable(this, "pipeline")
-
-    //Automatic checksums
-    for ((_, summarizableList) <- summarizables; summarizable <- summarizableList; (_, file) <- summarizable.summaryFiles) {
+    def addChecksum(file: File): Unit = {
       if (writeSummary.md5sum && !SummaryQScript.md5sumCache.contains(file)) {
         val md5sum = Md5sum(this, file)
         writeSummary.deps :+= md5sum.output
@@ -54,8 +57,28 @@ trait SummaryQScript extends BiopetQScript with Summarizable {
       //TODO: add more checksums types
     }
 
+    //Automatic checksums
+    for ((_, summarizableList) <- summarizables; summarizable <- summarizableList; (_, file) <- summarizable.summaryFiles)
+      addChecksum(file)
+
+    for ((_, sl) <- summarizables) {
+      for (s <- sl) {
+        s match {
+          case c: BiopetCommandLineFunctionTrait => {
+            executables += c.configName -> (new File(c.executable), c.getVersion)
+          }
+          case _ =>
+        }
+      }
+    }
+
+    for ((_, file) <- this.summaryFiles)
+      addChecksum(file)
+
     add(writeSummary)
   }
+
+  protected[summary] val executables: mutable.Map[String, (File, String)] = mutable.Map()
 }
 
 object SummaryQScript {

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -47,7 +47,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
 
   def summaryFiles = Map()
 
-  def summaryData = Map()
+  def summarySettings = Map()
 
   def makeSample(id: String) = new Sample(id)
   class Sample(sampleId: String) extends AbstractSample(sampleId) {

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

@@ -48,7 +48,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
       (if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> outputFiles("output_R2_gzip")) else Map())
   }
 
-  def summaryData = Map("skip_trim" -> skipTrim, "skip_clip" -> skipClip, "paired" -> paired)
+  def summarySettings = Map("skip_trim" -> skipTrim, "skip_clip" -> skipClip, "paired" -> paired)
 
   var paired: Boolean = input_R2.isDefined
   var R1_ext: String = _
@@ -136,6 +136,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     val seqtkSeq_R1 = SeqtkSeq(this, R1, swapExt(outDir, R1, R1_ext, ".sanger" + R1_ext), fastqc_R1)
     seqtkSeq_R1.isIntermediate = true
     add(seqtkSeq_R1)
+    addSummarizable(seqtkSeq_R1, "seqtkSeq_R1")
     R1 = seqtkSeq_R1.output
     deps ::= R1
 
@@ -143,6 +144,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
       val seqtkSeq_R2 = SeqtkSeq(this, R2, swapExt(outDir, R2, R2_ext, ".sanger" + R2_ext), fastqc_R2)
       seqtkSeq_R2.isIntermediate = true
       add(seqtkSeq_R2)
+      addSummarizable(seqtkSeq_R2, "seqtkSeq_R2")
       R2 = seqtkSeq_R2.output
       deps ::= R2
     }

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

@@ -96,7 +96,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
 
   def summaryFiles = Map()
 
-  def summaryData = Map()
+  def summarySettings = Map()
 
   def init() {
     require(outputDir != null, "Missing output directory on mapping module")