From e9215442ac12ff2f9ea4833b69daf809d8957cc6 Mon Sep 17 00:00:00 2001
From: Davy Cats <davycats.dc@gmail.com>
Date: Fri, 21 Oct 2022 15:14:04 +0200
Subject: [PATCH] fastp: use number of splits as number of threads if set
---
fastp.wdl | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/fastp.wdl b/fastp.wdl
index 25f09e3..7f269d8 100644
--- a/fastp.wdl
+++ b/fastp.wdl
@@ -38,8 +38,8 @@ task Fastp {
Boolean performAdapterTrimming = true
Int threads = 4
- String memory = "20GiB"
- Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 7.0 / threads)
+ String memory = "50GiB"
+ Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 6.0 / threads)
String dockerImage = "quay.io/biocontainers/fastp:0.23.2--h5f740d0_3"
}
@@ -66,7 +66,7 @@ task Fastp {
-z ~{compressionLevel} \
~{if correction then "--correction" else ""} \
--length_required ~{lengthRequired} \
- --thread ~{threads} \
+ --thread ~{select_first([split, threads])} \
~{"--split " + split} \
~{if defined(split) then "-d 0" else ""} \
~{if performAdapterTrimming then "" else "--disable_adapter_trimming"}
@@ -80,7 +80,7 @@ task Fastp {
}
runtime {
- cpu: threads
+ cpu: select_first([split, threads])
memory: memory
time_minutes: timeMinutes
docker: dockerImage
@@ -96,9 +96,9 @@ task Fastp {
compressionLevel: {description: "The compression level to use for the output.", category: "advanced"}
correction: {description: "Whether or not to apply overlap based correction.", category: "advanced"}
lengthRequired: {description: "The minimum read length.", category: "advanced"}
- split: {description: "The number of chunks to split the files into.", category: "common"}
+ split: {description: "The number of chunks to split the files into. Number of threads will be set equal to the amount of splits.", category: "common"}
performAdapterTrimming: {description: "Whether adapter trimming should be performed or not.", category: "advanced"}
- threads: {description: "The number of threads to use.", category: "advanced"}
+ threads: {description: "The number of threads to use. Only used if the split input is not set.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", 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"}
--
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