diff --git a/samtools.wdl b/samtools.wdl index ab2c84e2882603fa56f364110c0fe67d588a6f2a..8bdf771209c658f69892d71c294194f1b27064ee 100644 --- a/samtools.wdl +++ b/samtools.wdl @@ -26,7 +26,7 @@ task Index { input { String? preCommand File bamFile - String? bamIndexPath + String bamIndexPath } command { @@ -38,7 +38,7 @@ task Index { output { IndexedBamFile outputBam = object { file: bamFile, - index: select_first(flatten([[bamIndexPath], glob(sub(basename(bamFile), "\.bam$", "") + "*.bai")])) + index: bamIndexPath } } }