From ddae57644147098dda2d867029cb0af627e145fe Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 26 Jun 2020 09:15:13 +0200
Subject: [PATCH] Increase time estimates for sort tasks
---
picard.wdl | 2 +-
sambamba.wdl | 2 +-
samtools.wdl | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/picard.wdl b/picard.wdl
index f0f687f..f03535c 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 440b8f0..cccfddd 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 fbc491e..edcea9b 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)
--
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