Commit 8b320e53 authored by Sander Bollen's avatar Sander Bollen
Browse files

Merge branch 'fix-index_output_mergeSam' into 'develop'

Adding index file as output file for queue

Small fix to add the index file as output file for queue

See merge request !219
parents 784b647f 9ce8c169
......@@ -45,6 +45,14 @@ class MergeSamFiles(val root: Configurable) extends Picard {
@Argument(doc = "COMMENT", required = false)
var comment: Option[String] = config("comment")
@Output(doc = "Bam Index", required = true)
private var outputIndex: File = _
override def beforeGraph() {
if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
/** Returns command to execute */
override def commandLine = super.commandLine +
repeat("INPUT=", input, spaceSeparated = false) +
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