diff --git a/bwa.wdl b/bwa.wdl index 4cfd6fbe3863df222f626ecd8161b0ea460507de..0c35bf3aa5be30a2cad430debaa63f04f463b430 100644 --- a/bwa.wdl +++ b/bwa.wdl @@ -100,7 +100,7 @@ task Kit { # BWA needs slightly more memory than the size of the index files (~10%). Add a margin for safety here. Int memoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 1.2) + sortMemoryPerThreadGb * sortThreads Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 220 / threads) - # Contains bwa 0.7.17 bwakit 0.7.17.dev1 and samtools + # Contains bwa 0.7.17 bwakit 0.7.17.dev1 and samtools 1.10 String dockerImage = "quay.io/biocontainers/mulled-v2-ad317f19f5881324e963f6a6d464d696a2825ab6:c59b7a73c87a9fe81737d5d628e10a3b5807f453-0" } @@ -114,7 +114,7 @@ task Kit { ~{read1} \ ~{read2} \ 2> ~{outputPrefix}.log.bwamem | \ - k8 /opt/conda/bin/bwa-postalt.js \ + bwa-postalt.js \ -p ~{outputPrefix}.hla \ ~{bwaIndex.fastaFile}~{true=".64.alt" false=".alt" sixtyFour} | \ samtools sort \