Commit 9ce8c169 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding index file as output file for queue

parent 0ae99234
...@@ -45,6 +45,14 @@ class MergeSamFiles(val root: Configurable) extends Picard { ...@@ -45,6 +45,14 @@ class MergeSamFiles(val root: Configurable) extends Picard {
@Argument(doc = "COMMENT", required = false) @Argument(doc = "COMMENT", required = false)
var comment: Option[String] = config("comment") var comment: Option[String] = config("comment")
@Output(doc = "Bam Index", required = true)
private var outputIndex: File = _
override def beforeGraph() {
super.beforeGraph()
if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
}
/** Returns command to execute */ /** Returns command to execute */
override def commandLine = super.commandLine + override def commandLine = super.commandLine +
repeat("INPUT=", input, spaceSeparated = false) + repeat("INPUT=", input, spaceSeparated = false) +
......
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