From 3d59d9b820c25fcdd51ac537767f73c695850b6d Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 2 Apr 2020 15:24:44 +0200
Subject: [PATCH] rename time parameter
---
cutadapt.wdl | 6 +++---
fastqc.wdl | 6 +++---
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/cutadapt.wdl b/cutadapt.wdl
index bb04e33..5f51e9c 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -80,10 +80,10 @@ task Cutadapt {
Int compressionLevel = 1 # This only affects outputs with the .gz suffix.
Int cores = 4
String? memory
- Int? runtimeMinutes
+ Int? timeMinutes
String dockerImage = "quay.io/biocontainers/cutadapt:2.8--py37h516909a_0"
}
- Int estimatedRuntimeMin = 1 + ceil(size([read1, read2], "G") * 12.0 / cores)
+ Int estimatedTimeMinutes = 1 + ceil(size([read1, read2], "G") * 12.0 / cores)
String estimatedMemory = "~{300 + 100 * cores}M"
String realRead2output = select_first([read2output, "cut_r2.fq.gz"])
@@ -170,7 +170,7 @@ task Cutadapt {
runtime {
cpu: cores
memory: select_first([memory, estimatedMemory])
- runtime_minutes: select_first([runtimeMinutes, estimatedRuntimeMin])
+ time_minutes: select_first([timeMinutes, estimatedTimeMinutes])
docker: dockerImage
}
diff --git a/fastqc.wdl b/fastqc.wdl
index adc103e..fc93589 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -39,13 +39,13 @@ task Fastqc {
Int threads = 1
String? memory
- Int? runtimeMinutes
+ Int? timeMinutes
String dockerImage = "quay.io/biocontainers/fastqc:0.11.9--0"
Array[File]? NoneArray
File? NoneFile
}
String estimatedMemory = "~{250 + 250 * threads}M"
- Int estimatedRuntimeMin = 1 + ceil(size(seqFile, "G")) * 4
+ Int estimatedTimeMinutes = 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.
@@ -87,7 +87,7 @@ task Fastqc {
cpu: threads
memory: select_first([memory, estimatedMemory])
docker: dockerImage
- runtime_minutes: select_first([runtimeMinutes, estimatedRuntimeMin])
+ time_minutes: select_first([timeMinutes, estimatedTimeMinutes])
}
parameter_meta {
--
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