nf-core_modules/modules/pangolin/main.nf

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'

params.options = [:]
options        = initOptions(params.options)

process PANGOLIN {
    tag "$meta.id"
    label 'process_medium'
    publishDir "${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::pangolin=3.0.5' : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0'
    } else {
        container 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0'
    }

    input:
    tuple val(meta), path(fasta)

    output:
    tuple val(meta), path('*.csv'), emit: report
    path  '*.version.txt'         , emit: version

    script:
    def software = getSoftwareName(task.process)
    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
    """
    pangolin \\
        $fasta\\
        --outfile ${prefix}.pangolin.csv \\
        --threads $task.cpus \\
        $options.args

    echo \$(pangolin --version) | sed "s/pangolin //g" > ${software}.version.txt
    """
}