mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-27 14:19:55 +00:00
37 lines
1.1 KiB
Text
Generated
37 lines
1.1 KiB
Text
Generated
process BRACKEN_COMBINEBRACKENOUTPUTS {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda "bioconda::bracken=2.7"
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
|
|
'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(input)
|
|
|
|
output:
|
|
tuple val(meta), path("*.txt"), emit: txt
|
|
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}"
|
|
// WARN: Version information not provided by tool on CLI.
|
|
// Please update version string below when bumping container versions.
|
|
def VERSION = '2.7'
|
|
"""
|
|
combine_bracken_outputs.py \\
|
|
$args \\
|
|
--files ${input} \\
|
|
-o ${prefix}.txt
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
combine_bracken_output: ${VERSION}
|
|
END_VERSIONS
|
|
"""
|
|
}
|