vcftomaf/main.nf at 1151b85307367d36b3f337ebe39421e08033a7ef · famosab/vcftomaf · GitHub

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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    qbic-pipelines/vcftomaf
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/qbic-pipelines/vcftomaf
----------------------------------------------------------------------------------------
*/

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

include { VCFTOMAF                } from './workflows/vcftomaf'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

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

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

    //
    PIPELINE_COMPLETION(
        params.email,
        params.email_on_fail,
        params.plaintext_email,
        params.outdir,
        params.monochrome_logs,
        params.hook_url,
        QBICPIPELINES_VCFTOMAF.out.multiqc_report,
    )
}

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

//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow QBICPIPELINES_VCFTOMAF {
    take:
    samplesheet // channel: samplesheet read in from --input

    main:
    //
    // SET PARAMETERS
    //
    params.fasta = getGenomeAttribute('fasta')
    params.dict = getGenomeAttribute('dict')

    // Extra files
    intervals = params.intervals ? channel.fromPath(params.intervals).collect() : channel.value([])
    liftover_chain = params.liftover_chain ? channel.fromPath(params.liftover_chain).collect() : channel.value([])

    // FASTA
    fasta = params.fasta ? channel.fromPath(params.fasta).collect() : channel.value([])
    dict = params.dict ? channel.fromPath(params.dict).collect() : channel.empty()

    // VEP cache
    vep_cache = params.vep_cache ? channel.fromPath(params.vep_cache).collect() : channel.value([])
    vep_cache_unpacked = channel.value([])

    //
    // WORKFLOW: Run pipeline
    //

    VCFTOMAF(
        samplesheet,
        intervals,
        fasta,
        dict,
        liftover_chain,
        vep_cache,
        vep_cache_unpacked,
    )

    emit:
    multiqc_report = VCFTOMAF.out.multiqc_report // channel: /path/to/multiqc_report.html
}