taxprofiler/conf/modules.config

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

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

    withName: FASTP_SINGLE {
        ext.args   = [
            // trimming options
            params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
            params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
            // filtering options
            "--length_required ${params.shortread_clipmerge_minlength}"
        ].join(' ').trim()
        ext.prefix = { "${meta.id}_${meta.run_accession}" }
        publishDir = [
            path: { "${params.outdir}/fastp" },
            mode: 'copy',
            pattern: '*.fastq.gz'
        ]
    }

    withName: FASTP_PAIRED {
        ext.args   = [
            // collapsing options - option to retain singletons
            params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
            // trimming options
            params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
            params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
            params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : "--detect_adapter_for_pe",
            // filtering options
            "--length_required ${params.shortread_clipmerge_minlength}"
        ].join(' ').trim()
        ext.prefix = { "${meta.id}_${meta.run_accession}" }
        publishDir = [
            path: { "${params.outdir}/fastp" },
            mode: 'copy',
            pattern: '*.fastq.gz'
        ]
    }

    withName: ADAPTERREMOVAL_SINGLE {
        ext.args   = [
            // trimming options
            params.shortread_clipmerge_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
            params.shortread_clipmerge_adapter1 ? "--adapter1 ${params.shortread_clipmerge_adapter1}" : "",
            // filtering options
            "--minlength ${params.shortread_clipmerge_minlength}"
        ].join(' ').trim()
        ext.prefix = { "${meta.id}_${meta.run_accession}" }
        publishDir = [
            path: { "${params.outdir}/adapterremoval" },
            mode: 'copy',
            pattern: '*.fastq.gz'
        ]
    }

    withName: ADAPTERREMOVAL_PAIRED {
        ext.args   = [
            // collapsing options
            params.shortread_clipmerge_mergepairs ? "--collapse" : "",
            // trimming options
            params.shortread_clipmerge_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
            params.shortread_clipmerge_adapter1 ? "--adapter1 ${params.shortread_clipmerge_adapter1}" : "",
            params.shortread_clipmerge_adapter2 ? "--adapter2 ${params.shortread_clipmerge_adapter2}" : "",
            // filtering options
            "--minlength ${params.shortread_clipmerge_minlength}"
        ].join(' ').trim()
        ext.prefix = { "${meta.id}_${meta.run_accession}" }
        publishDir = [
            path: { "${params.outdir}/adapterremoval" },
            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: CAT_FASTQ {
        publishDir = [
            path: { "${params.outdir}/prepared_sequences" },
            mode: 'copy',
            pattern: '*.fastq.gz'
        ]
    }

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

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

    withName: METAPHLAN3 {
        publishDir = [
            path: { "${params.outdir}/metaphlan3/${meta.db_name}" },
            mode: params.publish_dir_mode,
            pattern: '*.{biom,txt}'
        ]
        ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
    }

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

}