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use broadinstitute container

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Rike 2022-06-09 15:06:46 +02:00
parent ef5b0dd977
commit b9e397ff15
1 changed files with 1 additions and 1 deletions
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modules/gatk4/markduplicatesspark/main.nf
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@ -5,7 +5,7 @@ process GATK4_MARKDUPLICATES_SPARK {
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" 'broadinstitute/gatk4:4.2.6.1' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)