--- a
+++ b/main.nf
@@ -0,0 +1,124 @@
+#!/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
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/