125 lines (111 with data), 3.5 kB

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

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { DEEPMODELOPTIM          } from './workflows/deepmodeloptim'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_deepmodeloptim_pipeline'
include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_deepmodeloptim_pipeline'

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

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

    take:
        data
        data_config
        model
        model_config
        initial_weights
        preprocessing_config
        genome
        tune_trials_range
        tune_replicates
        prediction_data

    main:

    //
    // WORKFLOW: Run pipeline
    //
    DEEPMODELOPTIM (
        data,
        data_config,
        model,
        model_config,
        initial_weights,
        preprocessing_config,
        genome,
        tune_trials_range,
        tune_replicates,
        prediction_data
    )
}

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

workflow {

    main:
    //
    // SUBWORKFLOW: Run initialisation tasks
    //
    PIPELINE_INITIALISATION (
        params.version,
        params.validate_params,
        params.monochrome_logs,
        args,
        params.outdir,
        // and the input files
        params.data,
        params.data_config,
        params.model,
        params.model_config,
        params.initial_weights,
        params.preprocessing_config
    )

    //
    // WORKFLOW: Run main workflow
    //
    NFCORE_DEEPMODELOPTIM (
        PIPELINE_INITIALISATION.out.data,
        PIPELINE_INITIALISATION.out.data_config,
        PIPELINE_INITIALISATION.out.model,
        PIPELINE_INITIALISATION.out.model_config,
        PIPELINE_INITIALISATION.out.initial_weights,
        PIPELINE_INITIALISATION.out.preprocessing_config,
        PIPELINE_INITIALISATION.out.genome,
        PIPELINE_INITIALISATION.out.tune_trials_range,
        PIPELINE_INITIALISATION.out.tune_replicates,
        PIPELINE_INITIALISATION.out.prediction_data
    )

    //
    // 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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/