fix merge request issues

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

@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Gather, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Gather, Output }
 
 class GenotypeGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.GenotypeGVCFs with GatkGeneral {
 

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala

@@ -17,10 +17,10 @@ class BcftoolsView(val root: Configurable) extends Bcftools {
   var output: File = _
 
   @Argument(doc = "drop individual genotypes", required = false)
-  var dropGenotype: Boolean = false
+  var dropGenotype: Boolean = config("drop_genotype", default = false)
 
   @Argument(doc = "header only", required = false)
-  var headerOnly: Boolean = false
+  var headerOnly: Boolean = config("header_only", false)
 
   @Argument(doc = "Compression level", required = false)
   var compressionLevel: Int = 9
@@ -29,88 +29,88 @@ class BcftoolsView(val root: Configurable) extends Bcftools {
   var outputType: String = "z"
 
   @Argument(doc = "regions", required = false)
-  var regions: String = _
+  var regions: Option[String] = config("r")
 
   @Argument(doc = "region file", required = false)
-  var regionFile: File = _
+  var regionFile: Option[File] = config("R")
 
   @Argument(doc = "targets", required = false)
-  var targets: String = _
+  var targets: Option[String] = config("t")
 
   @Argument(doc = "targets file", required = false)
-  var targetFile: File = _
+  var targetFile: Option[File] = config("T")
 
   @Argument(doc = "trim alt alleles", required = false)
-  var trimAltAlleles: Boolean = false
+  var trimAltAlleles: Boolean = config("trim_alt_allele", default = false)
 
   @Argument(doc = "no update", required = false)
-  var noUpdate: Boolean = false
+  var noUpdate: Boolean = config("no_update", default = false)
 
   @Argument(doc = "samples", required = false)
-  var samples: List[String] = Nil
+  var samples: List[String] = config("s", default = Nil)
 
   @Argument(doc = "samples file", required = false)
-  var sampleFile: File = _
+  var sampleFile: Option[File] = config("S")
 
   @Argument(doc = "minimum allele count", required = false)
-  var minAC: Option[Int] = _
+  var minAC: Option[Int] = config("c")
 
   @Argument(doc = "max allele count", required = false)
-  var maxAC: Option[Int] = _
+  var maxAC: Option[Int] = config("C")
 
   @Argument(doc = "exclude (expression)", required = false)
-  var exclude: String = _
+  var exclude: Option[String] = config("e")
 
   @Argument(doc = "apply filters", required = false)
-  var applyFilters: List[String] = Nil
+  var applyFilters: List[String] = config("F", default = Nil)
 
   @Argument(doc = "genotype", required = false)
-  var genotype: String = _
+  var genotype: Option[String] = config("g")
 
   @Argument(doc = "include (expression)", required = false)
-  var include: String = _
+  var include: Option[String] = config("i")
 
   @Argument(doc = "Known (ID field is not .) only", required = false)
-  var known: Boolean = false
+  var known: Boolean = config("k", default = false)
 
   @Argument(doc = "min alleles", required = false)
-  var minAlleles: Option[Int] = _
+  var minAlleles: Option[Int] = config("m")
 
   @Argument(doc = "max alleles", required = false)
-  var maxAlleles: Option[Int] = _
+  var maxAlleles: Option[Int] = config("M")
 
   @Argument(doc = "novel (ID field is .) only", required = false)
-  var novel: Boolean = false
+  var novel: Boolean = config("n", false)
 
   @Argument(doc = "phased only", required = false)
-  var phased: Boolean = false
+  var phased: Boolean = config("p", false)
 
   @Argument(doc = "exclude phased (only)", required = false)
-  var excludePhased: Boolean = false
+  var excludePhased: Boolean = config("P", false)
 
   @Argument(doc = "min allele frequency", required = false)
-  var minAF: Option[Int] = _
+  var minAF: Option[Int] = config("q")
 
   @Argument(doc = "max allele frequency", required = false)
-  var maxAF: Option[Int] = _
+  var maxAF: Option[Int] = config("Q")
 
   @Argument(doc = "uncalled only", required = false)
-  var uncalled: Boolean = false
+  var uncalled: Boolean = config("u", default = false)
 
   @Argument(doc = "exclude uncalled (only)", required = false)
-  var excludeUncalled: Boolean = false
+  var excludeUncalled: Boolean = config("U", default = false)
 
   @Argument(doc = "types", required = false)
-  var types: String = _
+  var types: Option[String] = config("v")
 
   @Argument(doc = "exclude types", required = false)
-  var excludeTypes: String = _
+  var excludeTypes: Option[String] = config("V")
 
   @Argument(doc = "private (requires samples)", required = false)
-  var onlyPrivate: Boolean = false
+  var onlyPrivate: Boolean = config("x", default = false)
 
   @Argument(doc = "Exclude privates", required = false)
-  var excludePrivate: Boolean = false
+  var excludePrivate: Boolean = config("X", default = false)
 
   override def beforeGraph() = {
     super.beforeGraph()
@@ -123,21 +123,39 @@ class BcftoolsView(val root: Configurable) extends Bcftools {
   }
 
   def baseCmd = {
-    executable + " view " + conditional(dropGenotype, "-G") + conditional(headerOnly, "-h") +
-      required("-l", compressionLevel) + required("-O", outputType) +
-      optional("-r", regions) + optional("-R", regionFile) +
-      optional("-t", targets) + optional("-T", targetFile) +
-      conditional(trimAltAlleles, "-a") + conditional(noUpdate, "-I") +
-      repeat("-s", samples) + optional("-S", sampleFile) +
-      optional("-c", minAC) + optional("-C", maxAC) +
-      optional("-e", exclude) + optional("-f", applyFilters) +
-      optional("-g", genotype) + optional("-i", include) +
-      conditional(known, "-k") + optional("-m", minAlleles) +
-      optional("-M", maxAlleles) + conditional(novel, "-n") +
-      conditional(phased, "-p") + conditional(excludePhased, "-P") +
-      optional("-q", minAF) + optional("-Q", maxAF) +
-      conditional(uncalled, "-u") + conditional(excludeUncalled, "-U") +
-      optional("-v", types) + conditional(onlyPrivate, "-x") +
+    executable +
+      required("view") +
+      conditional(dropGenotype, "-G") +
+      conditional(headerOnly, "-h") +
+      required("-l", compressionLevel) +
+      required("-O", outputType) +
+      optional("-r", regions) +
+      optional("-R", regionFile) +
+      optional("-t", targets) +
+      optional("-T", targetFile) +
+      conditional(trimAltAlleles, "-a") +
+      conditional(noUpdate, "-I") +
+      repeat("-s", samples) +
+      optional("-S", sampleFile) +
+      optional("-c", minAC) +
+      optional("-C", maxAC) +
+      optional("-e", exclude) +
+      optional("-f", applyFilters) +
+      optional("-g", genotype) +
+      optional("-i", include) +
+      conditional(known, "-k") +
+      optional("-m", minAlleles) +
+      optional("-M", maxAlleles) +
+      conditional(novel, "-n") +
+      conditional(phased, "-p") +
+      conditional(excludePhased, "-P") +
+      optional("-q", minAF) +
+      optional("-Q", maxAF) +
+      conditional(uncalled, "-u") +
+      conditional(excludeUncalled, "-U") +
+      optional("-v", types) +
+      optional("-V", excludeTypes) +
+      conditional(onlyPrivate, "-x") +
       conditional(excludePrivate, "-X")
   }
 

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala

@@ -14,7 +14,7 @@ class BedtoolsMerge(val root: Configurable) extends Bedtools {
   var input: File = _
 
   @Argument(doc = "Distance")
-  var dist: Int = 1 //default of tool is 1
+  var dist: Option[Int] = config("dist") //default of tool is 1
 
   @Output(doc = "Output bed file")
   var output: File = _

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala

@@ -13,9 +13,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Argument }
 abstract class Manwe extends BiopetCommandLineFunction {
   executable = config("exe", default = "manwe", submodule = "manwe")
 
-  override def defaultCoreMemory = 2.0
-  override def defaultThreads = 1
-
   var manweConfig: File = createManweConfig(None)
 
   @Output(doc = "the output file")
@@ -58,31 +55,28 @@ abstract class Manwe extends BiopetCommandLineFunction {
     val dataBufferSize: Option[Int] = config("varda_buffer_size", default = 1024 * 1024)
     val taskPollWait: Option[Int] = config("varda_task_poll_wait", default = 2)
 
-    val urlString = s"API_ROOT = '${url.toString}'"
-    val tokenString = s"TOKEN = '${token.toString}'"
-    val sslSettingString = sslSettings match {
-      case Some("true")  => "VERIFY_CERTIFICATE = True"
-      case Some("false") => "VERIFY_CERTIFICATE = False"
-      case Some(x)       => s"VERIFY_CERTIFICATE = '$x'"
-      case _             => "VERIFY_CERTIFICATE = True"
-    }
+    val settingsMap: Map[String, Any] = Map(
+      "API_ROOT" -> s"'$url'",
+      "TOKEN" -> s"'$token'",
+      "VERIFY_CERTIFICATE" -> (sslSettings match {
+        case Some("true")  => "True"
+        case Some("false") => "False"
+        case Some(x)       => s"'$x'"
+        case _             => "True"
+      }),
+      "COLLECTION_CACHE_SIZE" -> collectionCacheSize.getOrElse(20),
+      "DATA_BUFFER_SIZE" -> dataBufferSize.getOrElse(1048576),
+      "TASK_POLL_WAIT" -> taskPollWait.getOrElse(2)
+    )
 
-    val collectionString = s"COLLECTION_CACHE_SIZE = ${collectionCacheSize.getOrElse(20)}"
-    val dataString = s"DATA_BUFFER_SIZE = ${dataBufferSize.getOrElse(1048576)}"
-    val taskString = s"TASK_POLL_WAIT = ${taskPollWait.getOrElse(2)}"
     val file = directory match {
       case Some(dir) => File.createTempFile("manwe_config", ".py", dir)
       case None      => File.createTempFile("manwe_config", ".py")
     }
+
     file.deleteOnExit()
     val writer = new PrintWriter(file)
-    writer.println(urlString)
-    writer.println(tokenString)
-    writer.println(sslSettingString)
-    writer.println(collectionString)
-    writer.println(dataString)
-    writer.println(taskString)
-
+    settingsMap.foreach { case (key, value) => writer.println(s"$key = $value") }
     writer.close()
     file
   }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala

@@ -25,7 +25,8 @@ class ManweAnnotateBed(val root: Configurable) extends Manwe {
   def subCommand = {
     required("annotate-bed") + required(bed) +
       conditional(alreadyUploaded, "-u") +
-      repeat("-q", queries) + conditional(waitToComplete, "--wait")
+      repeat("-q", queries) +
+      conditional(waitToComplete, "--wait")
   }
 
 }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala

@@ -25,7 +25,8 @@ class ManweAnnotateVcf(val root: Configurable) extends Manwe {
   def subCommand = {
     required("annotate-vcf") + required(vcf) +
       conditional(alreadyUploaded, "-u") +
-      repeat("-q", queries) + conditional(waitToComplete, "--wait")
+      repeat("-q", queries) +
+      conditional(waitToComplete, "--wait")
   }
 
 }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala

@@ -19,7 +19,8 @@ class ManweDataSourcesAnnotate(val root: Configurable) extends Manwe {
 
   def subCommand = {
     required("data-sources") + required("annotate") +
-      required(uri) + repeat("-q", queries) +
+      required(uri) +
+      repeat("-q", queries) +
       conditional(waitToComplete, "--wait")
   }
 

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesDownload.scala

@@ -12,9 +12,8 @@ class ManweDataSourcesDownload(val root: Configurable) extends Manwe {
   var uri: String = _
 
   def subCommand = {
-    required("data-sources") + required("download") + required(uri)
+    required("data-sources") +
+      required("download") +
+      required(uri)
   }
-
-  this.deps
-
 }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala

@@ -14,7 +14,8 @@ class ManweDataSourcesList(val root: Configurable) extends Manwe {
   var user: Option[String] = _
 
   def subCommand = {
-    required("data-sources") + required("list") +
+    required("data-sources") +
+      required("list") +
       optional("-u", user)
   }
 

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala

@@ -14,7 +14,8 @@ class ManweDataSourcesShow(val root: Configurable) extends Manwe {
   var uri: Option[String] = _
 
   def subCommand = {
-    required("data-sources") + required("show") +
+    required("data-sources") +
+      required("show") +
       required(uri)
   }
 

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala

@@ -14,7 +14,8 @@ class ManweSamplesActivate(val root: Configurable) extends Manwe {
   var uri: String = _
 
   def subCommand = {
-    required("samples") + required("activate") +
+    required("samples") +
+      required("activate") +
       required(uri)
   }
 

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala

@@ -20,8 +20,11 @@ class ManweSamplesAdd(val root: Configurable) extends Manwe {
   var poolSize: Option[Int] = _
 
   def subCommand = {
-    required("samples") + required("add") + required(name) +
-      optional("-s", poolSize) + repeat("-g", group)
+    required("samples") +
+      required("add") +
+      required(name) +
+      optional("-s", poolSize) +
+      repeat("-g", group)
   }
 
 }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAnnotateVariations.scala

@@ -17,8 +17,10 @@ class ManweSamplesAnnotateVariations(val root: Configurable) extends Manwe {
   var queries: List[String] = Nil
 
   def subCommand = {
-    required("samples") + required("annotate-variations") +
-      required(uri) + repeat("-q", queries)
+    required("samples") +
+      required("annotate-variations") +
+      required(uri) +
+      repeat("-q", queries)
   }
 
 }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala

@@ -45,10 +45,16 @@ class ManweSamplesImport(val root: Configurable) extends Manwe {
   var waitToComplete: Boolean = false
 
   def subCommand = {
-    required("samples") + required("import") + required(name) +
-      repeat("-g", group) + repeat("--vcf", vcfs) + repeat("--bed", beds) +
-      optional("-s", poolSize) + conditional(alreadyUploaded, "-u") +
-      conditional(public, "-p") + conditional(preferLikelihood, "-l") +
+    required("samples") +
+      required("import") +
+      required(name) +
+      repeat("-g", group) +
+      repeat("--vcf", vcfs) +
+      repeat("--bed", beds) +
+      optional("-s", poolSize) +
+      conditional(alreadyUploaded, "-u") +
+      conditional(public, "-p") +
+      conditional(preferLikelihood, "-l") +
       conditional(noCoverage, "--no-coverage-profile") +
       conditional(waitToComplete, "--wait")
   }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala

@@ -27,9 +27,12 @@ class ManweSamplesImportBed(val root: Configurable) extends Manwe {
   var waitToComplete: Boolean = false
 
   def subCommand = {
-    required("samples") + required("import-bed") +
-      required(uri) + required(bed) +
-      conditional(alreadyUploaded, "-u") + conditional(waitToComplete, "--wait")
+    required("samples") +
+      required("import-bed") +
+      required(uri) +
+      required(bed) +
+      conditional(alreadyUploaded, "-u") +
+      conditional(waitToComplete, "--wait")
   }
 
 }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala

@@ -30,9 +30,11 @@ class ManweSamplesImportVcf(val root: Configurable) extends Manwe {
   var waitToComplete: Boolean = false
 
   def subCommand = {
-    required("samples") + required("import-vcf") +
+    required("samples") +
+      required("import-vcf") +
       required(uri) + required(vcf) +
-      conditional(alreadyUploaded, "-u") + conditional(preferLikelihoods, "-l") +
+      conditional(alreadyUploaded, "-u") +
+      conditional(preferLikelihoods, "-l") +
       conditional(waitToComplete, "--wait")
   }
 

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala

@@ -19,8 +19,11 @@ class ManweSamplesList(val root: Configurable) extends Manwe {
   var onlyPublic: Boolean = false
 
   def subCommand = {
-    required("samples") + required("list") + optional("-u", user) +
-      repeat("-g", group) + conditional(onlyPublic, "-p")
+    required("samples") +
+      required("list") +
+      optional("-u", user) +
+      repeat("-g", group) +
+      conditional(onlyPublic, "-p")
   }
 
 }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala

@@ -14,7 +14,9 @@ class ManweSamplesShow(val root: Configurable) extends Manwe {
   var uri: Option[String] = _
 
   def subCommand = {
-    required("samples") + required("show") + required(uri)
+    required("samples") +
+      required("show") +
+      required(uri)
   }
 
 }

public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala

@@ -334,14 +334,17 @@ class ManweTest extends TestNGSuite with Matchers {
     }
 
     val file: File = manwe.createManweConfig(None)
-    val contents = Source.fromFile(file).getLines().mkString("\n")
+    val contents = Source.fromFile(file).getLines().toList
 
-    contents should equal("""API_ROOT = 'http://127.0.0.1:5000'
-        |TOKEN = 'QWERTYUIOPASDFGHJKLZXCVBNM'
-        |VERIFY_CERTIFICATE = True
-        |COLLECTION_CACHE_SIZE = 25
-        |DATA_BUFFER_SIZE = 200
-        |TASK_POLL_WAIT = 5""".stripMargin)
+    val supposedContent = List("API_ROOT = 'http://127.0.0.1:5000'",
+      "TOKEN = 'QWERTYUIOPASDFGHJKLZXCVBNM'",
+      "VERIFY_CERTIFICATE = True",
+      "COLLECTION_CACHE_SIZE = 25",
+      "DATA_BUFFER_SIZE = 200",
+      "TASK_POLL_WAIT = 5"
+    )
+
+    supposedContent.sorted should equal(contents.sorted)
 
     val manwe2 = new ManweAnnotateBed(null) {
       override def globalConfig = new Config(Map(
@@ -354,15 +357,16 @@ class ManweTest extends TestNGSuite with Matchers {
     }
 
     val file2: File = manwe2.createManweConfig(None)
-    val contents2 = Source.fromFile(file2).getLines().mkString("\n")
-
-    contents2 should equal("""API_ROOT = 'http://127.0.0.1:5000'
-                            |TOKEN = 'QWERTYUIOPASDFGHJKLZXCVBNM'
-                            |VERIFY_CERTIFICATE = '/a/b/c/d.crt'
-                            |COLLECTION_CACHE_SIZE = 25
-                            |DATA_BUFFER_SIZE = 200
-                            |TASK_POLL_WAIT = 5""".stripMargin)
-
+    val contents2 = Source.fromFile(file2).getLines().toList
+    val supposedContent2 = List("API_ROOT = 'http://127.0.0.1:5000'",
+      "TOKEN = 'QWERTYUIOPASDFGHJKLZXCVBNM'",
+      "VERIFY_CERTIFICATE = '/a/b/c/d.crt'",
+      "COLLECTION_CACHE_SIZE = 25",
+      "DATA_BUFFER_SIZE = 200",
+      "TASK_POLL_WAIT = 5"
+    )
+
+    supposedContent2.sorted should equal(contents2.sorted)
   }
 
 }

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -186,7 +186,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
    */
   def varda(vcf: File, gVcf: File): File = {
 
-    val annotationQueries: List[String] = config("annotation_queries", default = Nil, submodule = "manwe")
+    val annotationQueries: List[String] = config("annotation_queries", default = List("GLOBAL *"), submodule = "manwe")
     //TODO: add groups!!! Need sample-specific group tags for this
 
     val annotate = new ManweAnnotateVcf(this)