mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-24 12:39:55 +00:00
33 lines
1.1 KiB
Text
Generated
33 lines
1.1 KiB
Text
Generated
process CENTRIFUGE_KREPORT {
|
|
tag "$meta.id"
|
|
label 'process_single'
|
|
|
|
conda "bioconda::centrifuge=1.0.4_beta"
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6':
|
|
'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
|
|
|
|
input:
|
|
tuple val(meta), path(report)
|
|
path db
|
|
|
|
output:
|
|
tuple val(meta), path('*.txt') , emit: kreport
|
|
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}"
|
|
"""
|
|
db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/\\.1.cf\$//'`
|
|
centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
|
|
END_VERSIONS
|
|
"""
|
|
}
|