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Commit 15343889 authored by cagaser's avatar cagaser
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add tmpDir input to specify temporary directory when sorting.

parent e9d123a9
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......@@ -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
......
......@@ -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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