Commit c82a2851 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added reference

parent 64cd8714
......@@ -16,6 +16,9 @@ class CollectTargetedPcrMetrics(val root: Configurable) extends Picard with Summ
@Input(doc = "The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: File = _
@Input(doc = "Reference", required = true)
var reference: File = config("reference")
@Input(doc = "AMPLICON_INTERVALS", required = true)
var ampliconIntervals: File = _
......@@ -37,6 +40,7 @@ class CollectTargetedPcrMetrics(val root: Configurable) extends Picard with Summ
override def commandLine = super.commandLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
required("REFERENCE_SEQUENCE=", reference, spaceSeparated = false) +
repeat("METRIC_ACCUMULATION_LEVEL=", metricAccumulationLevel, spaceSeparated = false) +
required("AMPLICON_INTERVALS=", ampliconIntervals, spaceSeparated = false) +
repeat("TARGET_INTERVALS=", targetIntervals, spaceSeparated = false) +
......
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