From 153438890ea1068846522b7e6386256bba48ab71 Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Mon, 12 Oct 2020 15:53:41 +0200
Subject: [PATCH] add tmpDir input to specify temporary directory when sorting.
---
CHANGELOG.md | 1 +
bcftools.wdl | 4 +++-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6c32d34..700bf0b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
++ bcftools: add tmpDir input to specify temporary directory when sorting.
+ bcftools: remove outputType and implement indexing based on output file extension.
+ NanoPack: Add parameter_meta to NanoPlot task.
+ Centrifuge: Remove metrics file from classification (which causes the
diff --git a/bcftools.wdl b/bcftools.wdl
index e225133..63f2cac 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -127,6 +127,7 @@ task Sort {
input {
File inputFile
String outputPath = "output.vcf.gz"
+ String tmpDir = "./sorting-tmp"
String memory = "256M"
Int timeMinutes = 1 + ceil(size(inputFile, "G"))
String dockerImage = "quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2"
@@ -136,10 +137,11 @@ task Sort {
command {
set -e
- mkdir -p "$(dirname ~{outputPath})"
+ mkdir -p "$(dirname ~{outputPath})" ~{tmpDir}
bcftools sort \
-o ~{outputPath} \
-O ~{true="z" false="v" compressed} \
+ -T ~{tmpDir} \
~{inputFile}
~{if compressed then 'bcftools index --tbi ~{outputPath}' else ''}
--
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