pipeline.nf

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    PRINT PARAMS SUMMARY
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'

def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
def summary_params = paramsSummaryMap(workflow)

// Print parameter summary log to screen
log.info logo + paramsSummaryLog(workflow) + citation

Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.initialise(params, log)

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    CONFIG FILES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    IMPORT LOCAL MODULES/SUBWORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
//
include { INPUT_CHECK } from '../subworkflows/local/input_check'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    IMPORT NF-CORE MODULES/SUBWORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
// MODULE: Installed directly from nf-core/modules
//
include { FASTQC                      } from '../modules/nf-core/fastqc/main'
include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

// Info required for completion email and summary
def multiqc_report = []

workflow {{ short_name|upper }} {

    ch_versions = Channel.empty()

    //
    // SUBWORKFLOW: Read in samplesheet, validate and stage input files
    //
    INPUT_CHECK (
        file(params.input)
    )
    ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
    // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input")
    // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/
    // ! There is currently no tooling to help you write a sample sheet schema

    //
    // MODULE: Run FastQC
    //
    FASTQC (
        INPUT_CHECK.out.reads
    )
    ch_versions = ch_versions.mix(FASTQC.out.versions.first())

    CUSTOM_DUMPSOFTWAREVERSIONS (
        ch_versions.unique().collectFile(name: 'collated_versions.yml')
    )

    //
    // MODULE: MultiQC
    //
    workflow_summary    = Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.paramsSummaryMultiqc(workflow, summary_params)
    ch_workflow_summary = Channel.value(workflow_summary)

    methods_description    = Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
    ch_methods_description = Channel.value(methods_description)

    ch_multiqc_files = Channel.empty()
    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
    ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))

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

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    COMPLETION EMAIL AND SUMMARY
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow.onComplete {
    if (params.email || params.email_on_fail) {
        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
    }
    NfcoreTemplate.dump_parameters(workflow, params)
    NfcoreTemplate.summary(workflow, params, log)
    if (params.hook_url) {
        NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
    }
}

workflow.onError {
    if (workflow.errorReport.contains("Process requirement exceeds available memory")) {
        println("🛑 Default resources exceed availability 🛑 ")
        println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡")
    }
}

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