LongTranscriptomics/main.nf at dev · number-25/LongTranscriptomics · GitHub

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#!/usr/bin/env nextflow

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    number-25/LongTranscriptomics
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/number-25/LongTranscriptomics
----------------------------------------------------------------------------------------
*/

nextflow.enable.dsl = 2

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

include { DIRECTRNA             } from './workflows/directrna'
include { validateParameters    } from 'plugin/nf-schema'
include { paramsSummaryLog      } from 'plugin/nf-schema'
include { paramsHelp            } from 'plugin/nf-schema'

workflow{

    //
    // nf-scheme validations
    //

    validateParameters()

    log.info paramsSummaryLog(workflow)

    if (params.help) {
        log.info paramsHelp(
            beforeText: "Welcome to LongTranscriptomics, I see you are seeking help. ",
            afterText: "Farewell, hopefully this was helpful.",
            command: "nextflow run . -profile <profile> --outdir <outdir>",
        )
        exit 0
    }

    DIRECTRNA ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
/*
workflow {

    main:

    PIPELINE_COMPLETION (
        params.email,
        params.email_on_fail,
        params.plaintext_email,
        params.outdir,
        params.monochrome_logs,
        params.hook_url,
        //MEDGEN_DIRECTRNA.out.multiqc_report
    )

}
*/

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