nf-core_modules/modules/blast/blastn/main.nf

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

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

process BLAST_BLASTN {
    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::blast=2.12.0' : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0'
    } else {
        container 'quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0'
    }

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

    output:
    tuple val(meta), path('*.blastn.txt'), emit: txt
    path "versions.yml"                  , emit: version

    script:
    def software = getSoftwareName(task.process)
    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
    """
    DB=`find -L ./ -name "*.ndb" | sed 's/.ndb//'`
    blastn \\
        -num_threads $task.cpus \\
        -db \$DB \\
        -query $fasta \\
        $options.args \\
        -out ${prefix}.blastn.txt
    cat <<-END_VERSIONS > versions.yml
    ${getProcessName(task.process)}:
        ${getSoftwareName(task.process)}: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
    END_VERSIONS
    """
}