nf-core_modules/modules/scoary/main.nf
Robert A. Petit III 22aa168622
add scoary module (#1034)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-06 16:34:39 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process SCOARY {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::scoary=1.6.16" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/scoary:1.6.16--py_2"
} else {
container "quay.io/biocontainers/scoary:1.6.16--py_2"
}
input:
tuple val(meta), path(genes), path(traits)
path(tree)
output:
tuple val(meta), path("*.csv"), emit: csv
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def newick_tree = tree ? "-n ${tree}" : ""
"""
scoary \\
$options.args \\
--no-time \\
--threads $task.cpus \\
--traits $traits \\
--genes $genes
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( scoary --version 2>&1 )
END_VERSIONS
"""
}