diff --git a/bwa-mem2.wdl b/bwa-mem2.wdl index b4ca877a0b9b9ed06acb396d47532500987f0893..4566e68c23e69a8a074d7849296962430e13fb60 100644 --- a/bwa-mem2.wdl +++ b/bwa-mem2.wdl @@ -34,8 +34,8 @@ task Mem { String? readgroup Int? sortThreads - Int? memoryGb Int threads = 4 + Int? memoryGb Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 220 / threads) # Contains bwa-mem2 2.0 bwakit 0.7.17.dev1 and samtools 1.10. String dockerImage = "quay.io/biocontainers/mulled-v2-6a15c99309c82b345497d24489bee67bbb76c2f6:1c9c3227b9bf825a8dc9726a25701aa23c0b1f12-0" @@ -101,8 +101,8 @@ task Mem { compressionLevel: {description: "The compression level of the output BAM.", category: "advanced"} readgroup: {description: "A readgroup identifier.", category: "common"} sortThreads: {description: "The number of threads to use for sorting.", category: "advanced"} - memoryGb: {description: "The amount of memory this job will use in gigabytes.", category: "advanced"} threads: {description: "The number of threads to use for alignment.", 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"}