Commit 4e003490 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed args for CollectGcBiasMetrics

parent 3f64deee
......@@ -35,7 +35,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summariza
@Output(doc = "Output chart", required = false)
var outputChart: File = _
@Output(doc = "Output summary", required = false)
@Output(doc = "Output summary", required = true)
var outputSummary: File = _
@Input(doc = "Reference file", required = false)
......@@ -67,7 +67,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summariza
required("OUTPUT=", output, spaceSeparated = false) +
optional("CHART_OUTPUT=", outputChart, spaceSeparated = false) +
required("REFERENCE_SEQUENCE=", reference, spaceSeparated = false) +
optional("SUMMARY_OUTPUT=", outputSummary, spaceSeparated = false) +
required("SUMMARY_OUTPUT=", outputSummary, spaceSeparated = false) +
optional("WINDOW_SIZE=", windowSize, spaceSeparated = false) +
optional("MINIMUM_GENOME_FRACTION=", minGenomeFraction, spaceSeparated = false) +
conditional(assumeSorted, "ASSUME_SORTED=TRUE") +
......@@ -86,6 +86,7 @@ object CollectGcBiasMetrics {
val collectGcBiasMetrics = new CollectGcBiasMetrics(root)
collectGcBiasMetrics.input :+= input
collectGcBiasMetrics.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".gcbiasmetrics")
collectGcBiasMetrics.outputSummary = new File(outputDir, input.getName.stripSuffix(".bam") + ".gcbiasmetrics.summary")
collectGcBiasMetrics
}
}
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment