nf-core_modules/modules/glimpse/chunk/main.nf

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process GLIMPSE_CHUNK {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::glimpse-bio=1.1.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h2ce4488_2':
'quay.io/biocontainers/glimpse-bio:1.1.1--hce55b13_1' }"
input:
tuple val(meta), path(input)
val region
output:
tuple val(meta), path("*.txt"), emit: chunk_chr
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def prefix = task.ext.prefix ?: "${meta.id}"
def args = task.ext.args ?: ""
def VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
GLIMPSE_chunk \\
$args \\
--input $input \\
--region $region \\
--thread $task.cpus \\
--output ${prefix}.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
glimpse: $VERSION
END_VERSIONS
"""
}