From da98e6649613768aeef4aa7d53db37963a1d2a14 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Fri, 17 Jan 2020 13:45:52 +0100
Subject: [PATCH] Rename cores to threads.
---
centrifuge.wdl | 12 +++++-------
1 file changed, 5 insertions(+), 7 deletions(-)
diff --git a/centrifuge.wdl b/centrifuge.wdl
index b22d396..5c9ef08 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -35,7 +35,7 @@ task Build {
Int? kmerCount
File? sizeTable
- Int cores = 5
+ Int threads = 5
String memory = "20G"
String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he860b03_3"
}
@@ -44,7 +44,7 @@ task Build {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
centrifuge-build \
- ~{"--threads " + cores} \
+ ~{"--threads " + threads} \
~{true="--nodc" false="" disableDifferenceCover} \
~{"--offrate " + offrate} \
~{"--ftabchars " + ftabChars} \
@@ -62,7 +62,7 @@ task Build {
}
runtime {
- cpu: cores
+ cpu: threads
memory: memory
docker: dockerImage
}
@@ -99,7 +99,7 @@ task Classify {
String? hostTaxIDs
String? excludeTaxIDs
- Int cores = 4
+ Int threads = 4
String memory = "16G"
String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he860b03_3"
}
@@ -114,7 +114,7 @@ task Classify {
~{true="--phred64" false="--phred33" phred64} \
~{"--min-hitlen " + minHitLength} \
~{"--met-file " + outputPrefix + "/" + outputName + "_alignment_metrics.tsv"} \
- ~{"--threads " + cores} \
+ ~{"--threads " + threads} \
~{"--trim5 " + trim5} \
~{"--trim3 " + trim3} \
~{"-k " + reportMaxDistinct} \
@@ -164,7 +164,6 @@ task Inspect {
Int? across
- Int cores = 1
String memory = "4G"
String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he860b03_3"
}
@@ -186,7 +185,6 @@ task Inspect {
}
runtime {
- cpu: cores
memory: memory
docker: dockerImage
}
--
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