mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
be798861c6
* add module for abricate * rename abricate/abricate to abricate/run * Update test.yml Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
34 lines
983 B
Text
34 lines
983 B
Text
process ABRICATE_RUN {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
|
|
'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(assembly)
|
|
|
|
output:
|
|
tuple val(meta), path("*.txt"), emit: report
|
|
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}"
|
|
"""
|
|
abricate \\
|
|
$assembly \\
|
|
$args \\
|
|
--threads $task.cpus > ${prefix}.txt
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|