From e3a17b699e5b93a25ebd8ec4cc71ae4b7eb70285 Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 12 May 2022 18:19:33 +0200 Subject: [PATCH] update version --- modules/gatk4/markduplicatesspark/main.nf | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf index a086cd7a..2ef91111 100644 --- a/modules/gatk4/markduplicatesspark/main.nf +++ b/modules/gatk4/markduplicatesspark/main.nf @@ -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 \\