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update version

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This commit is contained in:
Rike 2022-05-12 18:19:33 +02:00
parent 99880654bf
commit e3a17b699e
1 changed files with 3 additions and 5 deletions
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8
modules/gatk4/markduplicatesspark/main.nf
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@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES_SPARK {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'broadinstitute/gatk:4.2.3.0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@ -32,8 +32,6 @@ process GATK4_MARKDUPLICATES_SPARK {
avail_mem = task.memory.giga
}
"""
export SPARK_USER=spark3
gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\
$input_list \\
--output $prefix \\