main.nf

process EXTRACT_COMMUNITIES {
    tag "$meta"
    label 'process_single'

    conda "bioconda::samtools=1.17"
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
        'biocontainers/samtools:1.17--h00cdaf9_0' }"

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

    output:
    tuple val(meta), path ("*.fa"), emit: community_fasta
    path "versions.yml"            , emit: versions

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

    script:
    def args = task.ext.args ?: ''
    """
    samtools \\
        faidx \\
        $fasta \\
        \$(cat ${community}) > ${community}.fa
    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    END_VERSIONS
    """
}