From 5f7b02189ad35cb84fe595560894610986ea7f3d Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 12 May 2022 18:35:51 +0200 Subject: [PATCH] reverse again, why did tests pass before --- modules/gatk4/markduplicatesspark/main.nf | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf index 2ef91111..4e01cccf 100644 --- a/modules/gatk4/markduplicatesspark/main.nf +++ b/modules/gatk4/markduplicatesspark/main.nf @@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES_SPARK { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : + 'broadinstitute/gatk:4.2.3.0' }" input: tuple val(meta), path(bam) @@ -22,7 +22,7 @@ process GATK4_MARKDUPLICATES_SPARK { script: def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}.bam" + prefix = task.ext.prefix ?: "${meta.id}" def input_list = bam.collect{"--input $it"}.join(' ') def avail_mem = 3 @@ -32,6 +32,10 @@ process GATK4_MARKDUPLICATES_SPARK { avail_mem = task.memory.giga } """ + export SPARK_USER=spark3 + + + gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\ $input_list \\ --output $prefix \\