Commit 8a6f4376 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix free vars

parent d65a12e7
......@@ -41,22 +41,22 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
var bamList: Option[File] = config("bam_list")
@Input(required = false)
var targets: Option[File] = config("targets")
var targets: Option[File] = config("targets", freeVar = false)
@Input(required = false)
var samples: Option[File] = config("samples")
var samples: Option[File] = config("samples", freeVar = false)
@Input(required = false)
var populations: Option[File] = config("populations")
var populations: Option[File] = config("populations", freeVar = false)
@Input(required = false)
var cnvMap: Option[File] = config("cnv_map")
var cnvMap: Option[File] = config("cnv_map", freeVar = false)
@Input(required = false)
var trace: Option[File] = config("trace")
var trace: Option[File] = config("trace", freeVar = false)
@Input(required = false)
var failedAlleles: Option[File] = config("failed_alleles")
var failedAlleles: Option[File] = config("failed_alleles", freeVar = false)
@Input(required = false)
var observationBias: Option[File] = config("observation_bias")
......@@ -65,14 +65,14 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
var contaminationEstimates: Option[File] = config("contamination_estimates")
@Input(required = false)
var variantInput: Option[File] = config("variant_input")
var variantInput: Option[File] = config("variant_input", freeVar = false)
@Input(required = false)
var haplotypeBasisAlleles: Option[File] = config("haplotype_basis_alleles")
var haplotypeBasisAlleles: Option[File] = config("haplotype_basis_alleles", freeVar = false)
var pvar: Option[Int] = config("pvar")
var theta: Option[Int] = config("theta")
var ploidy: Option[Int] = config("ploidy")
var pvar: Option[Int] = config("pvar", freeVar = false)
var theta: Option[Int] = config("theta", freeVar = false)
var ploidy: Option[Int] = config("ploidy", freeVar = false)
var useBestNAlleles: Option[Int] = config("use_best_n_alleles")
var maxComplexGap: Option[Int] = config("max_complex_gap")
var minRepeatSize: Option[Int] = config("min_repeat_size")
......
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