structure.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

WorkflowStructure.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'
include { ALIGNMENT_MINIMAP2          } from '../subworkflows/local/alignment'
include { BCFTOOLS_VARIANT_CALL       } from '../subworkflows/local/variantcall'
include { VCFTOOLS_FILTER             } from '../subworkflows/local/vcftools_filter'
include { VCF_TO_STR		          } from '../subworkflows/local/pgdspider_conversion'
include { STR_RUN_PLOT		          } from '../subworkflows/local/str_run_plot'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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 STRUCTURE {

    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())

    
    ALIGNMENT_MINIMAP2 (
	INPUT_CHECK.out.reads,
	params.reference)

	BCFTOOLS_VARIANT_CALL(
        ALIGNMENT_MINIMAP2.out.bamnames.collect(),
	params.reference,
	ALIGNMENT_MINIMAP2.out.sampnames.collect())

        VCFTOOLS_FILTER(
        BCFTOOLS_VARIANT_CALL.out.vcf,
        params.thining,
        params.maxmissing)

	VCF_TO_STR(
	VCFTOOLS_FILTER.out.noncomp,
	params.thining,
	params.maxmissing)

    STR_RUN_PLOT(
        params.meta,
        VCFTOOLS_FILTER.out.noncomp,
        VCF_TO_STR.out.str
    )
	
    CUSTOM_DUMPSOFTWAREVERSIONS (
        ch_versions.unique().collectFile(name: 'collated_versions.yml')
    )

    //
    // MODULE: MultiQC
    //
    //workflow_summary    = WorkflowStructure.paramsSummaryMultiqc(workflow, summary_params)
    //ch_workflow_summary = Channel.value(workflow_summary)

    //methods_description    = WorkflowStructure.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)
    }
}

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