Commit c37b0388 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge branch 'develop' into fix-BIOPET-635

parents 598f2b3d af88febc
...@@ -99,7 +99,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction => ...@@ -99,7 +99,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
beforeGraph() beforeGraph()
internalBeforeGraph() internalBeforeGraph()
this.commandDirectory = this.jobOutputFile.getParentFile if (jobOutputFile != null) this.commandDirectory = this.jobOutputFile.getAbsoluteFile.getParentFile
super.freezeFieldValues() super.freezeFieldValues()
} }
......
...@@ -23,13 +23,13 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output } ...@@ -23,13 +23,13 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class BedtoolsIntersect(val parent: Configurable) extends Bedtools { class BedtoolsIntersect(val parent: Configurable) extends Bedtools {
@Input(doc = "Input file (bed/gff/vcf/bam)") @Input(doc = "Input file (bed/gff/vcf/bam)")
var input: File = null var input: File = _
@Input(doc = "Intersect file (bed/gff/vcf)") @Input(doc = "Intersect file (bed/gff/vcf)")
var intersectFile: File = null var intersectFile: File = _
@Output(doc = "output File") @Output(doc = "output File")
var output: File = null var output: File = _
@Argument(doc = "Min overlap", required = false) @Argument(doc = "Min overlap", required = false)
var minOverlap: Option[Double] = config("minoverlap") var minOverlap: Option[Double] = config("minoverlap")
...@@ -46,7 +46,8 @@ class BedtoolsIntersect(val parent: Configurable) extends Bedtools { ...@@ -46,7 +46,8 @@ class BedtoolsIntersect(val parent: Configurable) extends Bedtools {
} }
/** Returns command to execute */ /** Returns command to execute */
def cmdLine = required(executable) + required("intersect") + def cmdLine: String = required(executable) +
required("intersect") +
required(inputTag, input) + required(inputTag, input) +
required("-b", intersectFile) + required("-b", intersectFile) +
optional("-f", minOverlap) + optional("-f", minOverlap) +
......
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