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similar issues arise with bqsrspark, also use broadinstitute container

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This commit is contained in:
Rike 2022-06-09 15:29:00 +02:00
parent 8e8f4c9c51
commit 6a4732ef3b
2 changed files with 4 additions and 8 deletions
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6
modules/gatk4/applybqsrspark/main.nf
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@ -2,10 +2,8 @@ process GATK4_APPLYBQSR_SPARK {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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 'broadinstitute/gatk:4.2.6.1'
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)

6
modules/gatk4/baserecalibratorspark/main.nf
View file

@ -2,10 +2,8 @@ process GATK4_BASERECALIBRATOR_SPARK {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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 'broadinstitute/gatk:4.2.6.1'
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(input), path(input_index), path(intervals) tuple val(meta), path(input), path(input_index), path(intervals)