Changed run to library

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

@@ -26,20 +26,20 @@ trait MultiSampleQScript extends BiopetQScript {
     return runSingleSampleJobs(Configurable.any2map(samples(sample)))
   }
 
-  final def runRunsJobs(sampleConfig: Map[String, Any]): Map[String, Map[String, File]] = {
+  final def runLibraryJobs(sampleConfig: Map[String, Any]): Map[String, Map[String, File]] = {
     var output: Map[String, Map[String, File]] = Map()
     val sampleID = sampleConfig("ID")
-    if (sampleConfig.contains("runs")) {
-      val runs = Configurable.any2map(sampleConfig("runs"))
+    if (sampleConfig.contains("librarys")) {
+      val runs = Configurable.any2map(sampleConfig("librarys"))
       for ((key, value) <- runs) {
-        var run = Configurable.any2map(value)
-        if (!run.contains("ID")) run += ("ID" -> key)
-        if (run("ID") == key) {
-          output += key -> runSingleRunJobs(run, sampleConfig)
+        var library = Configurable.any2map(value)
+        if (!library.contains("ID")) library += ("ID" -> key)
+        if (library("ID") == key) {
+          output += key -> runSingleLibraryJobs(library, sampleConfig)
         } else logger.warn("Key is not the same as ID on value for run of sample: " + sampleID)
       }
     } else logger.warn("No runs found in config for sample: " + sampleID)
     return output
   }
-  def runSingleRunJobs(runConfig: Map[String, Any], sampleConfig: Map[String, Any]): Map[String, File]
+  def runSingleLibraryJobs(runConfig: Map[String, Any], sampleConfig: Map[String, Any]): Map[String, File]
 }

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

@@ -70,17 +70,17 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   // Called for each sample
   def runSingleSampleJobs(sampleConfig: Map[String, Any]): Map[String, List[File]] = {
     var outputFiles: Map[String, List[File]] = Map()
-    var runBamfiles: List[File] = List()
+    var libraryBamfiles: List[File] = List()
     var sampleID: String = sampleConfig("ID").toString
-    for ((run, runFiles) <- runRunsJobs(sampleConfig)) {
-      runBamfiles +:= runFiles("FinalBam")
+    for ((library, libraryFiles) <- runLibraryJobs(sampleConfig)) {
+      libraryBamfiles +:= libraryFiles("FinalBam")
     }
-    outputFiles += ("FinalBams" -> runBamfiles)
+    outputFiles += ("FinalBams" -> libraryBamfiles)
 
-    if (runBamfiles.size > 0) {
-      finalBamFiles ++= runBamfiles
+    if (libraryBamfiles.size > 0) {
+      finalBamFiles ++= libraryBamfiles
       val gatkVariantcalling = new GatkVariantcalling(this)
-      gatkVariantcalling.inputBams = runBamfiles
+      gatkVariantcalling.inputBams = libraryBamfiles
       gatkVariantcalling.outputDir = outputDir + sampleID + "/variantcalling/"
       gatkVariantcalling.init
       gatkVariantcalling.biopetScript
@@ -91,7 +91,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   }
 
   // Called for each run from a sample
-  def runSingleRunJobs(runConfig: Map[String, Any], sampleConfig: Map[String, Any]): Map[String, File] = {
+  def runSingleLibraryJobs(runConfig: Map[String, Any], sampleConfig: Map[String, Any]): Map[String, File] = {
     var outputFiles: Map[String, File] = Map()
     val runID: String = runConfig("ID").toString
     val sampleID: String = sampleConfig("ID").toString
@@ -100,7 +100,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
     if (runConfig.contains("inputtype")) inputType = runConfig("inputtype").toString
     else inputType = config("inputtype", default = "dna").toString
     if (runConfig.contains("R1")) {
-      val mapping = Mapping.loadFromRunConfig(this, runConfig, sampleConfig, runDir)
+      val mapping = Mapping.loadFromLibraryConfig(this, runConfig, sampleConfig, runDir)
       addAll(mapping.functions) // Add functions of mapping to curent function pool
 
       outputFiles += ("FinalBam" -> mapping.outputFiles("finalBamFile"))

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

@@ -288,7 +288,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
 object Mapping extends PipelineCommand {
   override val pipeline = "/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.class"
 
-  def loadFromRunConfig(root: Configurable, runConfig: Map[String, Any], sampleConfig: Map[String, Any], runDir: String): Mapping = {
+  def loadFromLibraryConfig(root: Configurable, runConfig: Map[String, Any], sampleConfig: Map[String, Any], runDir: String): Mapping = {
     val mapping = new Mapping(root)
 
     logger.debug("Mapping runconfig: " + runConfig)