nf-core_modules/modules/vsearch/usearchglobal/main.nf

// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
//               All other parameters MUST be provided using the "task.ext" directive, see here:
//               https://www.nextflow.io/docs/latest/process.html#ext
//               where "task.ext" is a string.
//               Any parameters that need to be evaluated in the context of a particular sample
//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
//               unless there is a run-time, storage advantage in implementing in this way
//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
//                 bwa mem | samtools view -B -T ref.fasta

process VSEARCH_USEARCHGLOBAL {
    tag '$queryfasta'
    label 'process_low'

    conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--hf1761c0_1':
        'quay.io/biocontainers/vsearch:2.21.1--h95f258a_0' }"

    input:
    path queryfasta
    path db
    val  outprefix

    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.

    output:
    path ("*.tsv")        , emit: tsv
    path "versions.yml"   , emit: versions

    when:
    task.ext.when == null || task.ext.when

    script:
    def args = task.ext.args ?: ''
    """
    vsearch \\
        --usearch_global $queryfasta \\
        --db $db \\
        --threads $task.cpus \\
        $args \\
        --blast6out ${outprefix}.tsv

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        vsearch: \$(vsearch --version 2>&1 | head -n 1 | sed 's/vsearch //g' | sed 's/,.*//g' | sed 's/^v//' | sed 's/_.*//')
    END_VERSIONS
    """
}