genomenote/main.nf at main · sanger-tol/genomenote · GitHub

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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    sanger-tol/genomenote
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/sanger-tol/genomenote
----------------------------------------------------------------------------------------
*/

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

include { GENOMENOTE  } from './workflows/genomenote'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_genomenote_pipeline'
include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_genomenote_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

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

    take:
    samplesheet     // channel: samplesheet read in from --input
    metadata        // channel: list of accession numbers to retrieve metadata for
    lineage_db      // channel: path to the Busco lineage, if provided
    ancestral_table // channel: path to the ancestral painting table, if provided
    cool_order      // channel: path to the ordered list of chromosomes, if provided
    btk_local_path  // channel: path of a local blobDir, if provided
    btk_online_path // channel: path of a remote blobDir, if provided

    main:

    //
    // WORKFLOW: Run pipeline
    //
    GENOMENOTE (
        samplesheet,
        metadata,
        lineage_db,
        ancestral_table,
        cool_order,
        btk_local_path,
        btk_online_path,
    )
    emit:
    multiqc_report = GENOMENOTE.out.multiqc_report // channel: /path/to/multiqc_report.html
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow {

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

    //
    // WORKFLOW: Run main workflow
    //
    SANGERTOL_GENOMENOTE (
        PIPELINE_INITIALISATION.out.samplesheet,
        PIPELINE_INITIALISATION.out.metadata,
        PIPELINE_INITIALISATION.out.lineage_db,
        PIPELINE_INITIALISATION.out.ancestral_table,
        PIPELINE_INITIALISATION.out.cool_order,
        PIPELINE_INITIALISATION.out.btk_local_path,
        PIPELINE_INITIALISATION.out.btk_online_path,
    )
    //
    // SUBWORKFLOW: Run completion tasks
    //
    PIPELINE_COMPLETION (
        params.email,
        params.email_on_fail,
        params.plaintext_email,
        params.outdir,
        params.monochrome_logs,
        params.hook_url,
        SANGERTOL_GENOMENOTE.out.multiqc_report
    )
}

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