diff --git a/picard.wdl b/picard.wdl index f0f687f04e2b02a12f88af0bd1369b68ac084f69..f03535c056bac0e60e214eb38fa3c8d4395c1ce1 100644 --- a/picard.wdl +++ b/picard.wdl @@ -669,7 +669,7 @@ task SortSam { # 4.000000001 which gets rounded to 5. # GATK Best practices uses 75000 here: https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/d2934ed656ade44801f9cfe1c0e78d4f80684b7b/PairedEndSingleSampleWf-fc-hg38.wdl#L778 Int XmxGb = ceil(maxRecordsInRam / 125001.0) - Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2) + Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3) # A mulled container is needed to have both picard and bwa in one container. # This container contains: picard (2.18.7), bwa (0.7.17-r1188) String dockerImage = "quay.io/biocontainers/picard:2.23.1--h37ae868_0" diff --git a/sambamba.wdl b/sambamba.wdl index 440b8f03e70a5430c9e921d318cc1616770dc1ec..cccfddd3db85f848b3ab6186c7de6113115100de 100644 --- a/sambamba.wdl +++ b/sambamba.wdl @@ -30,7 +30,7 @@ task Sort { Int memoryPerThreadGb = 4 Int memoryGb = 1 + threads * memoryPerThreadGb String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2" - Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2) + Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3) } # Select first needed as outputPath is optional input. (bug in cromwell) diff --git a/samtools.wdl b/samtools.wdl index fbc491ebdb31bbc6ba1edb957608f7db8d0fd297..edcea9be59f22a304096538ffc666f660fa359a5 100644 --- a/samtools.wdl +++ b/samtools.wdl @@ -373,7 +373,7 @@ task Sort { Int memoryPerThreadGb = 4 Int memoryGb = 1 + (threads + 1) * memoryPerThreadGb String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2" - Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2) + Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3) } # Select first needed as outputPath is optional input. (bug in cromwell)