Fixing config values

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

@@ -24,98 +24,98 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   override def versionCommand = executable + " " + vep_script + " --help"
 
   //Boolean vars
-  var v: Boolean = config("v")
-  var q: Boolean = config("q")
-  var offline: Boolean = config("offline")
-  var no_progress: Boolean = config("no_progress")
-  var everything: Boolean = config("everything")
-  var force: Boolean = config("force")
-  var no_stats: Boolean = config("no_stats")
-  var stats_text: Boolean = config("stats_text")
-  var html: Boolean = config("html")
-  var cache: Boolean = config("cache")
-  var humdiv: Boolean = config("humdiv")
-  var regulatory: Boolean = config("regulatory")
-  var cell_type: Boolean = config("cell_type")
-  var phased: Boolean = config("phased")
-  var allele_number: Boolean = config("allele_number")
-  var numbers: Boolean = config("numbers")
-  var domains: Boolean = config("domains")
-  var no_escape: Boolean = config("no_escape")
-  var hgvs: Boolean = config("hgvs")
-  var protein: Boolean = config("protein")
-  var symbol: Boolean = config("symbol")
-  var ccds: Boolean = config("ccds")
-  var uniprot: Boolean = config("uniprot")
-  var tsl: Boolean = config("tsl")
-  var canonical: Boolean = config("canonical")
-  var biotype: Boolean = config("biotype")
-  var xref_refseq: Boolean = config("xref_refseq")
-  var check_existing: Boolean = config("check_existing")
-  var check_alleles: Boolean = config("check_alleles")
-  var check_svs: Boolean = config("svs")
-  var gmaf: Boolean = config("gmaf")
-  var maf_1kg: Boolean = config("maf_1kg")
-  var maf_esp: Boolean = config("maf_esp")
-  var old_map: Boolean = config("old_maf")
-  var pubmed: Boolean = config("pubmed")
-  var failed: Boolean = config("failed")
+  var v: Boolean = config("v", default = true)
+  var q: Boolean = config("q", default = false)
+  var offline: Boolean = config("offline", default = false)
+  var no_progress: Boolean = config("no_progress", default = false)
+  var everything: Boolean = config("everything", default = true)
+  var force: Boolean = config("force", default = false)
+  var no_stats: Boolean = config("no_stats", default = false)
+  var stats_text: Boolean = config("stats_text", default = false)
+  var html: Boolean = config("html", default = false)
+  var cache: Boolean = config("cache", default = false)
+  var humdiv: Boolean = config("humdiv", default = false)
+  var regulatory: Boolean = config("regulatory", default = false)
+  var cell_type: Boolean = config("cell_type", default = false)
+  var phased: Boolean = config("phased", default = false)
+  var allele_number: Boolean = config("allele_number", default = false)
+  var numbers: Boolean = config("numbers", default = false)
+  var domains: Boolean = config("domains", default = false)
+  var no_escape: Boolean = config("no_escape", default = false)
+  var hgvs: Boolean = config("hgvs", default = false)
+  var protein: Boolean = config("protein", default = false)
+  var symbol: Boolean = config("symbol", default = false)
+  var ccds: Boolean = config("ccds", default = false)
+  var uniprot: Boolean = config("uniprot", default = false)
+  var tsl: Boolean = config("tsl", default = false)
+  var canonical: Boolean = config("canonical", default = false)
+  var biotype: Boolean = config("biotype", default = false)
+  var xref_refseq: Boolean = config("xref_refseq", default = false)
+  var check_existing: Boolean = config("check_existing", default = false)
+  var check_alleles: Boolean = config("check_alleles", default = false)
+  var check_svs: Boolean = config("svs", default = false)
+  var gmaf: Boolean = config("gmaf", default = false)
+  var maf_1kg: Boolean = config("maf_1kg", default = false)
+  var maf_esp: Boolean = config("maf_esp", default = false)
+  var old_map: Boolean = config("old_maf", default = false)
+  var pubmed: Boolean = config("pubmed", default = false)
+  var failed: Boolean = config("failed", default = false)
   var vcf: Boolean = config("vcf", default = true)
-  var json: Boolean = config("json")
-  var gvf: Boolean = config("gvf")
-  var check_ref: Boolean = config("check_ref")
-  var coding_only: Boolean = config("coding_only")
-  var no_intergenic: Boolean = config("no_intergenic")
-  var pick: Boolean = config("pick")
-  var pick_allele: Boolean = config("pick_allele")
-  var flag_pick: Boolean = config("flag_pick")
-  var flag_pick_allele: Boolean = config("flag_pick_allele")
-  var per_gene: Boolean = config("per_gene")
-  var most_severe: Boolean = config("most_severe")
-  var summary: Boolean = config("summary")
-  var filter_common: Boolean = config("filter_common")
-  var check_frequency: Boolean = config("check_frequency")
-  var allow_non_variant: Boolean = config("allow_non_variant")
-  var database: Boolean = config("database")
-  var genomes: Boolean = config("genomes")
-  var gencode_basic: Boolean = config("gencode_basic")
-  var refseq: Boolean = config("refseq")
-  var merged: Boolean = config("merged")
-  var all_refseq: Boolean = config("all_refseq")
-  var lrg: Boolean = config("lrg")
-  var no_whole_genome: Boolean = config("no_whole_genome")
-  var skip_db_check: Boolean = config("skip_db_check")
+  var json: Boolean = config("json", default = false)
+  var gvf: Boolean = config("gvf", default = false)
+  var check_ref: Boolean = config("check_ref", default = false)
+  var coding_only: Boolean = config("coding_only", default = false)
+  var no_intergenic: Boolean = config("no_intergenic", default = false)
+  var pick: Boolean = config("pick", default = false)
+  var pick_allele: Boolean = config("pick_allele", default = false)
+  var flag_pick: Boolean = config("flag_pick", default = false)
+  var flag_pick_allele: Boolean = config("flag_pick_allele", default = false)
+  var per_gene: Boolean = config("per_gene", default = false)
+  var most_severe: Boolean = config("most_severe", default = false)
+  var summary: Boolean = config("summary", default = false)
+  var filter_common: Boolean = config("filter_common", default = false)
+  var check_frequency: Boolean = config("check_frequency", default = false)
+  var allow_non_variant: Boolean = config("allow_non_variant", default = false)
+  var database: Boolean = config("database", default = false)
+  var genomes: Boolean = config("genomes", default = false)
+  var gencode_basic: Boolean = config("gencode_basic", default = false)
+  var refseq: Boolean = config("refseq", default = false)
+  var merged: Boolean = config("merged", default = false)
+  var all_refseq: Boolean = config("all_refseq", default = false)
+  var lrg: Boolean = config("lrg", default = false)
+  var no_whole_genome: Boolean = config("no_whole_genome", default = false)
+  var skip_db_check: Boolean = config("skip_db_check", default = false)
 
   // Textual args
-  var vep_config: String = config("config")
-  var species: String = config("species")
-  var assembly: String = config("assembly")
-  var format: String = config("format")
-  var dir: String = config("dir")
-  var dir_cache: String = config("dir_cache")
-  var dir_plugins: String = config("dir_plugins")
-  var fasta: File = config("fasta")
-  var sift: String = config("sift")
-  var polyphen: String = config("polyphen")
-  var custom: String = config("custom")
-  var plugin: List[String] = config("plugin")
-  var individual: String = config("individual")
-  var fields: String = config("fields")
-  var convert: String = config("convert")
-  var terms: String = config("terms")
-  var chr: String = config("chr")
-  var pick_order: String = config("pick_order")
-  var freq_pop: String = config("check_pop")
-  var freq_gt_lt: String = config("freq_gt_lt")
-  var freq_filter: String = config("freq_filter")
-  var filter: String = config("filter")
-  var host: String = config("host")
-  var user: String = config("user")
-  var password: String = config("password")
-  var registry: String = config("registry")
-  var build: String = config("build")
-  var compress: String = config("compress")
-  var cache_region_size: String = config("cache_region_size")
+  var vep_config: Option[String] = config("config")
+  var species: Option[String] = config("species")
+  var assembly: Option[String] = config("assembly")
+  var format: Option[String] = config("format")
+  var dir: Option[String] = config("dir")
+  var dir_cache: Option[String] = config("dir_cache")
+  var dir_plugins: Option[String] = config("dir_plugins")
+  var fasta: Option[String] = config("fasta")
+  var sift: Option[String] = config("sift")
+  var polyphen: Option[String] = config("polyphen")
+  var custom: Option[String] = config("custom")
+  var plugin: List[String] = config("plugin", default = Nil)
+  var individual: Option[String] = config("individual")
+  var fields: Option[String] = config("fields")
+  var convert: Option[String] = config("convert")
+  var terms: Option[String] = config("terms")
+  var chr: Option[String] = config("chr")
+  var pick_order: Option[String] = config("pick_order")
+  var freq_pop: Option[String] = config("check_pop")
+  var freq_gt_lt: Option[String] = config("freq_gt_lt")
+  var freq_filter: Option[String] = config("freq_filter")
+  var filter: Option[String] = config("filter")
+  var host: Option[String] = config("host")
+  var user: Option[String] = config("user")
+  var password: Option[String] = config("password")
+  var registry: Option[String] = config("registry")
+  var build: Option[String] = config("build")
+  var compress: Option[String] = config("compress")
+  var cache_region_size: Option[String] = config("cache_region_size")
 
   // Numeric args
   var fork: Option[Int] = config("fork")
@@ -129,7 +129,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
     super.afterGraph
     if (!cache && !database) {
       throw new IllegalArgumentException("Must supply either cache or database")
-    } else if (cache && dir == null) {
+    } else if (cache && dir.isEmpty) {
       throw new IllegalArgumentException("Must supply dir to cache")
     }
   }

public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala

@@ -24,7 +24,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
     nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp,
     nl.lumc.sasc.biopet.pipelines.sage.Sage,
     nl.lumc.sasc.biopet.pipelines.kopisu.ConiferPipeline,
-    nl.lumc.sasc.biopet.pipelines.carp.Carp
+    nl.lumc.sasc.biopet.pipelines.carp.Carp,
+    nl.lumc.sasc.biopet.pipelines.toucan.Toucan
   )
 
   def tools: List[MainCommand] = List(

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

@@ -4,6 +4,7 @@ import nl.lumc.sasc.biopet.core.{ PipelineCommand, BiopetQScript }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
 import nl.lumc.sasc.biopet.tools.VEPNormalizer
+import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
 
@@ -20,7 +21,11 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript {
 
   }
 
-  defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true))
+  override def defaults = ConfigUtils.mergeMaps(Map(
+    "varianteffectpredictor" -> Map("everything" -> true)
+  ), super.defaults)
+
+  //defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true))
 
   def biopetScript(): Unit = {
     val vep = new VariantEffectPredictor(this)