diff --git a/bwa.wdl b/bwa.wdl index f79a219a36e465e8a40eb137d9eb5cda34712d08..a129ebb444f74d55c90ae0bab2290635cb58f736 100644 --- a/bwa.wdl +++ b/bwa.wdl @@ -119,7 +119,7 @@ task Index { input { File fasta } - File indexedFile = "reference.fasta" + String indexedFile = "reference.fasta" command { set -e @@ -128,9 +128,9 @@ task Index { } output { - BwaIndex index = { - "fastaFile": indexedFile, - "indexFiles": [ + BwaIndex index = object { + fastaFile: indexedFile, + indexFiles: [ indexedFile + ".amb", indexedFile + ".ann", indexedFile + ".bwt", @@ -139,4 +139,10 @@ task Index { ] } } + + runtime { + docker: "quay.io/biocontainers/bwa:0.7.17--hed695b0_7" + cpu: 1 + memory: "~{size(fasta, 'G') + 1}GiB" + } } \ No newline at end of file