diff --git a/picard.wdl b/picard.wdl index e88172f9a360b07d58cbc4274b49927a65020968..f1c4a58ff26894fc53a481c3ad199fee4dd9665c 100644 --- a/picard.wdl +++ b/picard.wdl @@ -204,11 +204,9 @@ task GatherBamFiles { } output { - IndexedBamFile outputBam = object { - file: outputBamPath, - index: sub(outputBamPath, ".bam$", ".bai"), - md5: outputBamPath + ".md5" - } + File outputBam = outputBamPath + File outputBamIndex = sub(outputBamPath, ".bam$", ".bai") + File outputBamMd5 = outputBamPath + ".md5" } runtime { @@ -429,10 +427,8 @@ task SortVcf { } output { - IndexedVcfFile outputVcf = object { - file: outputVcfPath, - index: outputVcfPath + ".tbi" - } + File outputVcf = outputVcfPath + File outputVcfIndex = outputVcfPath + ".tbi" } runtime {