diff --git a/samtools.wdl b/samtools.wdl index 0d43015794579ba27f7ce58d7d3b144ea778f58f..ab2c84e2882603fa56f364110c0fe67d588a6f2a 100644 --- a/samtools.wdl +++ b/samtools.wdl @@ -36,10 +36,9 @@ task Index { } output { - File index = select_first(flatten([[bamIndexPath], glob(sub(basename(bamFile), "\.bam$", "") + "*.bai")])) IndexedBamFile outputBam = object { file: bamFile, - index: index + index: select_first(flatten([[bamIndexPath], glob(sub(basename(bamFile), "\.bam$", "") + "*.bai")])) } } }