diff --git a/bwa.wdl b/bwa.wdl index cc8ea0c673a1b8dd30aff212783b472cbfab739c..670f00d2d959e9c0fefa8e85a382708f1a812714 100644 --- a/bwa.wdl +++ b/bwa.wdl @@ -48,7 +48,7 @@ task Mem { Int estimatedSortThreads = if threads == 1 then 1 else 1 + ceil(threads / 4.0) Int totalSortThreads = select_first([sortThreads, estimatedSortThreads]) # BWA needs slightly more memory than the size of the index files (~10%). Add a margin for safety here. - Int estimatedMemoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 2) + sortMemoryPerThreadGb * totalSortThreads + Int estimatedMemoryGb = 10 + ceil(size(bwaIndex.indexFiles, "G") * 3) + sortMemoryPerThreadGb * totalSortThreads # The bwa postalt script is out commented as soon as usePostalt = false. # This hack was tested with bash, dash and ash. It seems that comments in between pipes work for all of them.