/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Config file for defining DSL2 per module options and publishing paths
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Available keys to override module options:
        ext.args   = Additional arguments appended to command in module.
        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
        ext.prefix = File name prefix for output files.
----------------------------------------------------------------------------------------
*/

process {

    publishDir = [
        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
        mode: params.publish_dir_mode,
        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
    ]

    withName: SAMPLESHEET_CHECK {
        publishDir = [
            path: { "${params.outdir}/pipeline_info" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
        ]
    }

    withName: FASTQC {
        ext.args = '--quiet'
        ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
        publishDir = [
            path: { "${params.outdir}/fastqc/raw" },
            mode: 'copy',
            pattern: '*.html'
        ]
    }

    withName: FASTP {
        ext.prefix = { "${meta.id}_${meta.run_accession}" }
        // TODO also include option to NOT merge
        ext.args   = [
            { ${meta.single_end} } == 0 ? "-m" : '',
            params.fastp_exclude_unmerged ? '' : "--include_unmerged"
        ].join(' ').trim()
        publishDir = [
            path: { "${params.outdir}/fastp" },
            mode: 'copy',
            pattern: '*.fastq.gz'
        ]
    }

    withName: PORECHOP {
        ext.prefix = { "${meta.id}_${meta.run_accession}" }
        publishDir = [
            path: { "${params.outdir}/porechop" },
            mode: 'copy',
            pattern: '*.fastq.gz'
        ]
    }

    withName: FASTQC_POST {
        ext.args = '--quiet'
        ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
        publishDir = [
            path: { "${params.outdir}/fastqc/processed" },
            mode: 'copy',
            pattern: '*.html'
        ]
    }

    withName: CAT_FASTQ {
        publishDir = [
            path: { "${params.outdir}/prepared_sequences" },
            mode: 'copy',
            pattern: '*.fastq.gz'
        ]
    }

    withName: MALT_RUN {
        publishDir = [
            path: { "${params.outdir}/malt/${meta.db_name}" },
            mode: 'copy',
            pattern: '*.{rma6,tab,text,sam,log}'
        ]
        ext.args = { "${meta.db_params}" }
        ext.when = params.run_malt
    }

    withName: KRAKEN2_KRAKEN2 {
        publishDir = [
            path: { "${params.outdir}/kraken2/${meta.db_name}" },
            mode: 'copy',
            pattern: '.{fastq.gz,txt}'
        ]
        ext.args = { "${meta.db_params}" }
        ext.when = params.run_kraken2
        ext.prefix = { "${meta.id}-${meta.db_name}" }
    }

    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
        publishDir = [
            path: { "${params.outdir}/pipeline_info" },
            mode: params.publish_dir_mode,
            pattern: '*_versions.yml'
        ]
    }

}