somalierextract-module.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: Optional inputs are not currently supported by Nextflow. However, using an empty
//               list (`[]`) instead of a file can be used to work around this issue.

process SOMALIER_EXTRACT {
    tag "$meta.id"
    label 'process_low'

    // TODO nf-core: List required Conda package(s).
    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
    conda (params.enable_conda ? "YOUR-TOOL-HERE" : null)
    // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
    //     'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
    //     'quay.io/biocontainers/YOUR-TOOL-HERE' }"


    input:
    tuple val(meta), path(bam), path(bai)
    path(ref)
    path(refidx)
    path(sites)

	output:
    tuple val(meta), path("${prefix}.somalier.extract/*.somalier"),     emit: extract
    path "versions.yml",                                                emit: versions

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

    script:
    def args = task.ext.args ?: ''
    prefix = task.ext.prefix ?: "${meta.id}"

    script:
	"""
    somalier_dbg4 extract -d ${prefix}.somalier.extract \
    --sites ${sites} \
    -f ${ref} \
    ${bam}

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        somalier: \$(echo \$(somalier_dbg4 2>&1) | sed 's/^.*somalier version: //; s/Commands:.*\$//')
    END_VERSIONS
	"""

}