You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
35 lines
1.0 KiB
Plaintext
35 lines
1.0 KiB
Plaintext
process KRAKENTOOLS_COMBINEKREPORTS {
|
|
label 'process_single'
|
|
|
|
conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
|
|
'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(kreports)
|
|
|
|
output:
|
|
tuple val(meta), path("*.txt"), emit: txt
|
|
path "versions.yml", emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
prefix = task.ext.prefix ?: "${meta.id}"
|
|
def VERSION = '1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
"""
|
|
combine_kreports.py \\
|
|
-r ${kreports} \\
|
|
-o ${prefix}.txt \\
|
|
${args}
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
combine_kreports.py: ${VERSION}
|
|
END_VERSIONS
|
|
"""
|
|
}
|