main.nf

#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    nf-core/eisca
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/nf-core/eisca
    Website: https://nf-co.re/eisca
    Slack  : https://nfcore.slack.com/channels/eisca
----------------------------------------------------------------------------------------
*/

nextflow.enable.dsl = 2

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

include { EISCA  } from './workflows/eisca'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_eisca_pipeline'
include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_eisca_pipeline'

include { GET_PARAMS              } from './modules/local/get_params'
include { MAKE_REPORT             } from './modules/local/make_report'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

// TODO nf-core: Remove this line if you don't need a FASTA file
//   This is an example of how to use getGenomeAttribute() to fetch parameters
//   from igenomes.config using `--genome`
// params.fasta = getGenomeAttribute('fasta')

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

// analyses = params.analyses.split(',').toList()
// skip_analyses = params.skip? params.skip.split(',').toList() : []

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

    take:
    samplesheet // channel: samplesheet read in from --input

    main:

    //
    // WORKFLOW: Run pipeline
    //
    EISCA (
        samplesheet
    )

    ch_results = Channel.fromPath(params.outdir)
    // if (params.analyses.contains('secondary') || params.analyses.contains('tertiary')){
    if (!params.run_analyses.intersect(['secondary', 'tertiary', 'annotation', 'dea', 'trajectory']).isEmpty()){    
        // GET_PARAMS()
        MAKE_REPORT (
            ch_results,
            Channel.fromPath(params.input),
            EISCA.out.multiqc_report,
            // EISCA.out.versions,
            // GET_PARAMS.out.json,
        )        
    }

    emit:
    multiqc_report = EISCA.out.multiqc_report // channel: /path/to/multiqc_report.html

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

workflow {

    main:

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

    //
    // WORKFLOW: Run main workflow
    //
    NFCORE_EISCA (
        PIPELINE_INITIALISATION.out.samplesheet
    )

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

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