curationpretext/main.nf at 9fa7e0af8e83145788c2514d022a051ed35be788 · sanger-tol/curationpretext · GitHub

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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    sanger-tol/curationpretext
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/sanger-tol/curationpretext
    Website: https://pipelines.tol.sanger.ac.uk/curationpretext
----------------------------------------------------------------------------------------
*/

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

include { CURATIONPRETEXT           } from './workflows/curationpretext'
include { PIPELINE_INITIALISATION   } from './subworkflows/local/utils_nfcore_curationpretext_pipeline'
include { PIPELINE_COMPLETION       } from './subworkflows/local/utils_nfcore_curationpretext_pipeline'

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


//
// WORKFLOW: Run main sanger-tol/curationpretext analysis pipeline
//
workflow SANGER_TOL_CURATIONPRETEXT {
    take:
    input_fasta
    reads
    cram
    teloseq

    main:

    CURATIONPRETEXT (
        input_fasta,
        reads,
        cram,
        teloseq
    )
    // CURATIONPRETEXT_MAPS
}

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

workflow {

    //
    // SUBWORKFLOW: Run initialisation tasks
    //
    PIPELINE_INITIALISATION (
        params.version,
        params.validate_params,
        params.monochrome_logs,
        args,
        params.outdir,
        [],                      // We are not using the samplesheet for this pipeline
        params.help,
        params.help_full,
        params.show_hidden
    )

    // MOVE THE CHANNEL CREATION INTO THE PIPELINE INITIALISATION

    //
    // WORFKLOW: Run main sanger-tol/curationpretext analysis pipeline
    //
    SANGER_TOL_CURATIONPRETEXT (
        PIPELINE_INITIALISATION.out.ch_reference,
        PIPELINE_INITIALISATION.out.ch_reads,
        PIPELINE_INITIALISATION.out.ch_cram_reads,
        PIPELINE_INITIALISATION.out.teloseq
    )

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

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