Remove required from config calls

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala

@@ -13,13 +13,13 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
 
   override def subPath = "gatk" :: super.subPath
 
-  jarFile = config("gatk_jar", required = true)
+  jarFile = config("gatk_jar")
 
   override val defaultVmem = "7G"
 
   if (config.contains("intervals")) intervals = config("intervals").asFileList
   if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
-  reference_sequence = config("reference", required = true)
+  reference_sequence = config("reference")
   if (config.contains("gatk_key")) gatk_key = config("gatk_key")
   if (config.contains("pedigree")) pedigree = config("pedigree").asFileList
 }

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

@@ -35,7 +35,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   var jointGenotyping: Boolean = config("joint_genotyping", default = false)
 
   var singleSampleCalling = config("single_sample_calling", default = true)
-  var reference: File = config("reference", required = true)
+  var reference: File = config("reference")
   var useAllelesOption: Boolean = config("use_alleles_option", default = false)
   val externalGvcfs = config("external_gvcfs_files", default = Nil).asFileList
 

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

@@ -30,7 +30,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
   var rawVcfInput: File = _
 
   @Argument(doc = "Reference", shortName = "R", required = false)
-  var reference: File = config("reference", required = true)
+  var reference: File = config("reference")
 
   @Argument(doc = "OutputName", required = false)
   var outputName: String = _

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

@@ -51,7 +51,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
   var functions: Seq[QFunction]
 
   final def script() {
-    outputDir = config("output_dir", required = true)
+    outputDir = config("output_dir")
     if (!outputDir.endsWith("/")) outputDir += "/"
     init
     biopetScript

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

@@ -29,7 +29,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
   var R2: File = _
 
   @Input(doc = "The reference file for the bam files.", shortName = "R")
-  var reference: File = config("reference", required = true)
+  var reference: File = config("reference")
 
   @Output(doc = "Output file SAM", shortName = "output")
   var output: File = _

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

@@ -29,13 +29,13 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
   var R2: File = _
 
   @Input(doc = "The reference file for the bam files.", shortName = "ref")
-  var reference: File = config("reference", required = true)
+  var reference: File = config("reference")
 
   @Input(doc = "The genome prefix.")
-  var genome: File = config("genome", required = true)
+  var genome: File = config("genome")
 
   @Input(doc = "The hash prefix")
-  var hash: File = config("hash", required = true)
+  var hash: File = config("hash")
 
   @Output(doc = "Output file SAM", shortName = "output")
   var output: File = _

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

@@ -29,7 +29,7 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
   var R2: File = _
 
   @Input(doc = "Bowtie index", shortName = "bti")
-  var bowtie_index: File = config("bowtie_index", required = true)
+  var bowtie_index: File = config("bowtie_index")
 
   @Argument(doc = "Output Directory")
   var outputDir: String = _

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala

@@ -13,7 +13,7 @@ class BwaAln(val root: Configurable) extends Bwa {
   var fastq: File = _
 
   @Input(doc = "The reference file for the bam files.", required = true)
-  var reference: File = config("reference", required = true)
+  var reference: File = config("reference")
 
   @Output(doc = "Output file SAM", required = false)
   var output: File = _

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala

@@ -29,7 +29,7 @@ class BwaMem(val root: Configurable) extends Bwa {
   var R2: File = _
 
   @Input(doc = "The reference file for the bam files.", shortName = "R")
-  var reference: File = config("reference", required = true)
+  var reference: File = config("reference")
 
   @Output(doc = "Output file SAM", shortName = "output")
   var output: File = _

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala

@@ -26,7 +26,7 @@ class BwaSampe(val root: Configurable) extends Bwa {
   var saiR2: File = _
 
   @Input(doc = "The reference file for the bam files.", required = true)
-  var reference: File = config("reference", required = true)
+  var reference: File = config("reference")
 
   @Output(doc = "Output file SAM", required = false)
   var output: File = _

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala

@@ -16,7 +16,7 @@ class BwaSamse(val root: Configurable) extends Bwa {
   var sai: File = _
 
   @Input(doc = "The reference file for the bam files.", required = true)
-  var reference: File = config("reference", required = true)
+  var reference: File = config("reference")
 
   @Output(doc = "Output file SAM", required = false)
   var output: File = _

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala

@@ -35,7 +35,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
   var outputSummary: File = _
 
   @Argument(doc = "Reference file", required = false)
-  var reference: File = config("reference", required = true)
+  var reference: File = config("reference")
 
   @Argument(doc = "Window size", required = false)
   var windowSize: Option[Int] = config("windowsize")

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala

@@ -30,9 +30,6 @@ class ConfigTest extends TestNGSuite with Matchers with ConfigUtils.ImplicitConv
   @Test def testApply: Unit = {
     ConfigTest.config("m1", Nil, "k1").asString shouldBe "v2"
     ConfigTest.config("m1", Nil, "notexist", default = "default").asString shouldBe "default"
-    intercept[IllegalStateException] {
-      ConfigTest.config("m1", Nil, "notexist")
-    }
   }
 
   @Test def testMergeConfigs: Unit = {

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala

@@ -27,10 +27,6 @@ class ConfigurableTest extends TestNGSuite with Matchers {
     classC.classB.get("k1").asString shouldBe "c1"
     classC.classB.classA.get("k1").asString shouldBe "c1"
 
-    classC.get("notexist") shouldBe null
-    intercept[IllegalStateException] {
-      classC.get("notexist", required = true)
-    }
     classC.get("notexist", default = "default").asString shouldBe "default"
 
     classC.get("k1", freeVar = false).asString shouldBe "c1"
@@ -47,11 +43,10 @@ abstract class Cfg extends Configurable {
   def get(key: String,
           default: String = null,
           submodule: String = null,
-          required: Boolean = false,
           freeVar: Boolean = true,
           sample: String = null,
           library: String = null) = {
-    config(key, default, submodule, required, freeVar = freeVar, sample = sample, library = library)
+    config(key, default, submodule, freeVar = freeVar, sample = sample, library = library)
   }
 }
 

public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

@@ -60,7 +60,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
     def makeLibrary(id: String) = new Library(id)
     class Library(libId: String) extends AbstractLibrary(libId) {
-      val inputFastq: File = config("R1", required = true)
+      val inputFastq: File = config("R1")
       val prefixFastq: File = createFile(".prefix.fastq")
 
       val flexiprep = new Flexiprep(qscript)

public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala

@@ -35,7 +35,7 @@ import org.broadinstitute.gatk.queue.engine.JobRunInfo
 class Yamsvp(val root: Configurable) extends QScript with BiopetQScript { //with MultiSampleQScript {
   def this() = this(null)
 
-  var reference: File = config("reference", required = true)
+  var reference: File = config("reference")
   var finalBamFiles: List[File] = Nil
   /*
   class LibraryOutput extends AbstractLibraryOutput {