mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
8002e373b5
* not yet working: add db version to versions.yml * next try: db version number not in versions.yml * Fix amrfinderplus versioning * Update main.nf * Apply suggestions from code review * Update main.nf * Dump version for syncrony with run * Update test.yml * Apply suggestions from code review Co-authored-by: James Fellows Yates <jfy133@gmail.com>
29 lines
904 B
Text
29 lines
904 B
Text
process AMRFINDERPLUS_UPDATE {
|
|
tag "update"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0':
|
|
'quay.io/biocontainers/ncbi-amrfinderplus:3.10.30--h6e70893_0' }"
|
|
|
|
output:
|
|
path "amrfinderdb.tar.gz", emit: db
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
"""
|
|
mkdir amrfinderdb
|
|
amrfinder_update -d amrfinderdb
|
|
tar czvf amrfinderdb.tar.gz -C \$(readlink amrfinderdb/latest) ./
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
amrfinderplus: \$(amrfinder --version)
|
|
END_VERSIONS
|
|
"""
|
|
}
|