main.nf

#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    UPHL-BioNGS/Grandeur
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/UPHL-BioNGS/Grandeur
----------------------------------------------------------------------------------------
*/

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

include { INITIALIZE } from './subworkflows/local/initialize'
include { GRANDEUR   } from './workflows/grandeur'


/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow {

  main:
  //
  // SUBWORKFLOW: Initialize files and tasks
  //
  INITIALIZE ()

  //
  // WORKFLOW: Run main workflow
  //
  GRANDEUR (
    INITIALIZE.out.reads,
    INITIALIZE.out.fastas,
    INITIALIZE.out.fastani_genomes,
    INITIALIZE.out.versions,
    INITIALIZE.out.genome_sizes,
    INITIALIZE.out.mash_db,
    INITIALIZE.out.kraken2_db,
    INITIALIZE.out.blast_db,
    INITIALIZE.out.dataset_script,
    INITIALIZE.out.evaluat_script,
    INITIALIZE.out.jsoncon_script,
    INITIALIZE.out.multiqc_script,
    INITIALIZE.out.summary_script,
    INITIALIZE.out.summfle_script,
    INITIALIZE.out.version_script
  )


}

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



workflow.onComplete {
  println("Pipeline completed at: $workflow.complete")
  println("MultiQC report can be found at ${params.outdir}/multiqc/multiqc_report.html")
  println("Summary can be found at ${params.outdir}/grandeur_summary.tsv")
  println("Execution status: ${ workflow.success ? 'OK' : 'failed' }")
}