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fix conda with openjdk 1.8

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This commit is contained in:
SusiJo 2022-06-09 10:24:39 +02:00
parent 0204d2374b
commit cda434611f
1 changed files with 2 additions and 1 deletions
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3
modules/gatk4/markduplicatesspark/main.nf
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@ -2,7 +2,7 @@ process GATK4_MARKDUPLICATES_SPARK {
tag "$meta.id" tag "$meta.id"
label 'process_high' label 'process_high'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0 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/gatk4:4.2.3.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'broadinstitute/gatk:4.2.3.0' }" 'broadinstitute/gatk:4.2.3.0' }"
@ -45,6 +45,7 @@ process GATK4_MARKDUPLICATES_SPARK {
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
openjdk: \$(echo \$(java -version 2>&1) | grep version | sed 's/\"//g' | cut -f3 -d ' ')
END_VERSIONS END_VERSIONS
""" """
} }