nf-core_modules/modules/hamronization/abricate/main.nf

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process HAMRONIZATION_ABRICATE {
tag "$meta.id"
label 'process_single'
conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
input:
tuple val(meta), path(report)
val(format)
val(software_version)
val(reference_db_version)
output:
tuple val(meta), path("*.json"), optional: true, emit: json
tuple val(meta), path("*.tsv") , optional: true, emit: tsv
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
hamronize \\
abricate \\
${report} \\
$args \\
--format ${format} \\
--analysis_software_version ${software_version} \\
--reference_database_version ${reference_db_version} \\
> ${prefix}.${format}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
END_VERSIONS
"""
}