diff --git a/samtools.wdl b/samtools.wdl index 8a5e065594062c92064fd3f82702e1e51a9e270f..ff2daf0d74058fab973c1b523c6bc1553aa71734 100644 --- a/samtools.wdl +++ b/samtools.wdl @@ -25,22 +25,22 @@ task BgzipAndIndex { task Index { input { String? preCommand - File bamFilePath + File bamFile String? bamIndexPath } command { set -e -o pipefail ~{preCommand} - samtools index ~{bamFilePath} ~{bamIndexPath} + samtools index ~{bamFile} ~{bamIndexPath} } output { IndexedBamFile outputBam = object { - file: bamFilePath, + file: bamFile, index: if defined(bamIndexPath) then select_first([bamIndexPath]) - else bamFilePath + ".bai" + else bamFile + ".bai" } } }