mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
fix conda with openjdk 1.8
This commit is contained in:
parent
0204d2374b
commit
cda434611f
1 changed files with 2 additions and 1 deletions
|
@ -2,7 +2,7 @@ process GATK4_MARKDUPLICATES_SPARK {
|
|||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0 conda-forge::openjdk=8.0.312" : null)
|
||||
container "${ 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' }"
|
||||
|
@ -45,6 +45,7 @@ process GATK4_MARKDUPLICATES_SPARK {
|
|||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
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
|
||||
"""
|
||||
}
|
||||
|
|
Loading…
Reference in a new issue