Commit 5f23d851 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing failing jobs

parent 0519d4f2
......@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
class CoverageStats(val parent: Configurable) extends PythonCommandLineFunction with Summarizable {
setPythonScript("nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py")
setPythonScript("bedtools_cov_stats.py")
@Input(doc = "Input file", required = false)
var input: File = _
......
......@@ -35,11 +35,13 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
*/
def setPythonScript(script: String) {
pythonScript = new File(script).getAbsoluteFile
if (!PythonCommandLineFunction.alreadyCopied.contains(script)) {
if (!PythonCommandLineFunction.alreadyCopied.contains((this.getClass, script))) {
setPythonScript(script, "")
PythonCommandLineFunction.alreadyCopied += script
this.getClass
PythonCommandLineFunction.alreadyCopied += (this.getClass, script) -> pythonScript
} else {
pythonScriptName = script
pythonScript = PythonCommandLineFunction.alreadyCopied((this.getClass, script))
}
}
......@@ -71,5 +73,5 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
}
object PythonCommandLineFunction {
private val alreadyCopied: mutable.Set[String] = mutable.Set()
private val alreadyCopied: mutable.Map[(Class[_], String), File] = mutable.Map()
}
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