main.nf

#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    nf-core/references
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/nf-core/references
    Website: https://nf-co.re/references
    Slack  : https://nfcore.slack.com/channels/references
----------------------------------------------------------------------------------------
*/

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { paramsSummaryMap        } from 'plugin/nf-schema'
include { methodsDescriptionText  } from './subworkflows/local/utils_nfcore_references_pipeline'
include { paramsSummaryMultiqc    } from './subworkflows/nf-core/utils_nfcore_pipeline'
include { softwareVersionsToYAML  } from './subworkflows/nf-core/utils_nfcore_pipeline'

include { MULTIQC                 } from './modules/nf-core/multiqc/main'

include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_references_pipeline'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_references_pipeline'

include { REFERENCES              } from "./workflows/references/main"

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow NFCORE_REFERENCES{

    take:
    input // channel: samplesheet read in from --input

    main:

    reports = Channel.empty()
    versions = Channel.empty()

    // WORKFLOW: Run pipeline
    REFERENCES(input, params.tools)

    versions = versions.mix(REFERENCES.out.versions)

    emit:
    versions
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow {

    main:
    //
    // SUBWORKFLOW: Run initialisation tasks
    //
    PIPELINE_INITIALISATION (
        params.version,
        params.validate_params,
        params.monochrome_logs,
        args,
        params.outdir,
        params.input
    )

    //
    // WORKFLOW: Run main workflow
    //
    NFCORE_REFERENCES(PIPELINE_INITIALISATION.out.samplesheet)

    ch_multiqc_files = Channel.empty()

    version_yaml = softwareVersionsToYAML(NFCORE_REFERENCES.out.versions)
        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_references_software_mqc_versions.yml', sort: true, newLine: true)

    //
    // MODULE: MultiQC
    //
    ch_multiqc_config                     = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
    ch_multiqc_custom_config              = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
    summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
    ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
    ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
    ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
    ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
    ch_multiqc_files                      = ch_multiqc_files.mix(version_yaml)
    ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true))

    MULTIQC (
        ch_multiqc_files.collect(),
        ch_multiqc_config.toList(),
        ch_multiqc_custom_config.toList(),
        ch_multiqc_logo.toList(),
        [],
        []
    )
    multiqc_report = MULTIQC.out.report.toList()

    //
    // SUBWORKFLOW: Run completion tasks
    //
    PIPELINE_COMPLETION (
        params.email,
        params.email_on_fail,
        params.plaintext_email,
        params.outdir,
        params.monochrome_logs,
        params.hook_url,
        multiqc_report
    )
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/