treeval/main.nf at main · sanger-tol/treeval · GitHub

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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    sanger-tol/treeval
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/sanger-tol/treeval
----------------------------------------------------------------------------------------
*/

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { PIPELINE_INITIALISATION       } from './subworkflows/local/utils_nfcore_treeval_pipeline'
include { PIPELINE_COMPLETION           } from './subworkflows/local/utils_nfcore_treeval_pipeline'
include { TREEVAL as SANGERTOL_TREEVAL  } from './workflows/treeval'

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

workflow {

    main:

    params.mode      = params.mode ?: "FULL"
    params.binfile   = params.binfile ?: false
    params.juicer    = params.juicer ?: false
    params.run_hires = params.run_hires ?: true

    //
    // SUBWORKFLOW: Run initialisation tasks
    //
    PIPELINE_INITIALISATION (
        params.version,
        params.validate_params,
        params.monochrome_logs,
        args,
        params.outdir,
        params.input,
        params.mode,
        params.binfile,
        params.juicer,
        params.run_hires
    )

    //
    // WORKFLOW: Run main workflow
    //
    SANGERTOL_TREEVAL (
        PIPELINE_INITIALISATION.out.assembly_id,
        PIPELINE_INITIALISATION.out.reference,
        PIPELINE_INITIALISATION.out.map_order,
        PIPELINE_INITIALISATION.out.assem_reads,
        PIPELINE_INITIALISATION.out.kmer_prof_file,
        PIPELINE_INITIALISATION.out.hic_reads,
        PIPELINE_INITIALISATION.out.supp_reads,
        PIPELINE_INITIALISATION.out.align_genesets,
        PIPELINE_INITIALISATION.out.synteny_paths,
        PIPELINE_INITIALISATION.out.intron_size,
        PIPELINE_INITIALISATION.out.teloseq,
        PIPELINE_INITIALISATION.out.lineageinfo,
        PIPELINE_INITIALISATION.out.lineagespath,
        PIPELINE_INITIALISATION.out.binfile,
        PIPELINE_INITIALISATION.out.juicer,
        PIPELINE_INITIALISATION.out.mode,
        PIPELINE_INITIALISATION.out.run_hires
    )

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