From 802b65e68ad7b8bcd700649eabd62cbc66b3944c Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 2 Apr 2020 14:25:09 +0200
Subject: [PATCH] make estimates overrideable
---
fastqc.wdl | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/fastqc.wdl b/fastqc.wdl
index 7e693f6..b1a587c 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -38,11 +38,14 @@ task Fastqc {
String? dir
Int threads = 1
- String memory = "1G"
+ String? memory
+ Int? runtimeMinutes
String dockerImage = "quay.io/biocontainers/fastqc:0.11.9--0"
Array[File]? NoneArray
File? NoneFile
}
+ String estimatedMemoryMB = "~{250 + 250 * threads}M"
+ Int estimatedRuntimeMin = 1 + ceil(size(seqFile, "G")) * 4
# Chops of the .gz extension if present.
# The Basename needs to be taken here. Otherwise paths might differ between similar jobs.
@@ -80,12 +83,11 @@ task Fastqc {
Array[File]? images = if extract then glob(reportDir + "/Images/*.png") else NoneArray
}
- Int estimatedRuntime = 1 + ceil(size(seqFile, "G")) * 4
runtime {
cpu: threads
- memory: memory
+ memory: select_first([memory, estimatedMemoryMB])
docker: dockerImage
- runtime_minutes: estimatedRuntime
+ runtime_minutes: select_first([runtimeMinutes, estimatedRuntimeMin])
}
parameter_meta {
--
GitLab