Commit f1d14870 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed default

parent 659f81e6
......@@ -46,7 +46,7 @@ class CollectMultipleMetrics(val parent: Configurable)
@Argument(doc = "Base name of output files", required = true)
var program: List[Programs.Value] = {
val value: List[String] = config("metrics_programs")
val value: List[String] = config("metrics_programs", default = Nil)
value match {
case Nil => Programs.values.toList
case list => list.flatMap(x => Programs.values.find(_.toString.toLowerCase == x.toLowerCase))
......@@ -107,17 +107,17 @@ class CollectMultipleMetrics(val parent: Configurable)
summarizable(
() =>
Picard.getMetrics(new File(outputName + ".alignment_summary_metrics"),
groupBy = Some("CATEGORY"))),
groupBy = Some("CATEGORY"))),
Programs.CollectAlignmentSummaryMetrics.toString,
forceSingle = true)
forceSingle = true
)
case Programs.CollectInsertSizeMetrics =>
qscript.addSummarizable(
summarizable(
() =>
if (new File(outputName + ".insert_size_metrics").exists())
Map(
"metrics" -> Picard.getMetrics(
new File(outputName + ".insert_size_metrics")),
"metrics" -> Picard.getMetrics(new File(outputName + ".insert_size_metrics")),
"histogram" -> Picard.getHistogram(
new File(outputName + ".insert_size_metrics"))
)
......@@ -130,7 +130,8 @@ class CollectMultipleMetrics(val parent: Configurable)
summarizable(
() => Picard.getHistogram(new File(outputName + ".quality_distribution_metrics"))),
Programs.QualityScoreDistribution.toString,
forceSingle = true)
forceSingle = true
)
case Programs.MeanQualityByCycle =>
qscript.addSummarizable(
summarizable(
......@@ -142,9 +143,10 @@ class CollectMultipleMetrics(val parent: Configurable)
summarizable(
() =>
Picard.getHistogram(new File(outputName + ".base_distribution_by_cycle_metrics"),
tag = "METRICS CLASS")),
tag = "METRICS CLASS")),
Programs.CollectBaseDistributionByCycle.toString,
forceSingle = true)
forceSingle = true
)
case _ => None
}
}
......
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