diff --git a/bwa.wdl b/bwa.wdl index 14b9a005f61a321899d4dfc7845ea49a01fce1aa..3f1276d1e35c45211149d58ab76418a9e8ed7b9e 100644 --- a/bwa.wdl +++ b/bwa.wdl @@ -92,7 +92,7 @@ task Kit { Boolean sixtyFour = false Int threads = 4 - String memory = 1 + ceil(size(bwaIndex.indexFiles, "G")) + String memoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G")) Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 220 / threads) String dockerImage = "biocontainers/bwakit:v0.7.15_cv1" } @@ -121,7 +121,7 @@ task Kit { # One extra thread for bwa-postalt + samtools is not needed. # These only use 5-10% of compute power and not always simultaneously. cpu: threads - memory: memory + memory: "~{memoryGb}G" time_minutes: timeMinutes docker: dockerImage } @@ -136,7 +136,7 @@ task Kit { sixtyFour: {description: "Whether or not the index uses the '.64' suffixes.", category: "common"} threads: {description: "The number of threads to use for alignment.", category: "advanced"} - memory: {description: "The amount of memory this job will use.", category: "advanced"} + memoryGb: {description: "The amount of memory this job will use in gigabytes.", category: "advanced"} timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"} dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}