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Commit 34a00edf authored by Sander Bollen's avatar Sander Bollen
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Fixing config values

parent 9dbde99d
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Showing with 98 additions and 92 deletions
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @ 34a00edf
......@@ -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
View file @ 34a00edf
......@@ -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
View file @ 34a00edf
......@@ -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)
......
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