preprocessing/main.nf at main · mvheetve/preprocessing · GitHub

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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing
----------------------------------------------------------------------------------------
*/

nextflow.enable.dsl = 2

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

params.bowtie2     = WorkflowMain.getGenomeAttribute(params, "bowtie2")
params.bwamem      = WorkflowMain.getGenomeAttribute(params, "bwa"    )
params.bwamem2     = WorkflowMain.getGenomeAttribute(params, "bwamem2")
params.dragmap     = WorkflowMain.getGenomeAttribute(params, "dragmap")
params.snap        = WorkflowMain.getGenomeAttribute(params, "snap"   )
params.fai         = WorkflowMain.getGenomeAttribute(params, "fai"    )
params.fasta       = WorkflowMain.getGenomeAttribute(params, "fasta"  )
params.dict        = WorkflowMain.getGenomeAttribute(params, "dict"   )

params.genelists   = WorkflowMain.getGenomeAttribute(params, "genelists")

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    VALIDATE & PRINT PARAMETER SUMMARY
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { validateParameters; paramsHelp } from 'plugin/nf-validation'

// Print help message if needed
if (params.help) {
    def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
    def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
    def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
    log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
    System.exit(0)
}

// Validate input parameters
if (params.validate_params) {
    validateParameters()
}

WorkflowMain.initialise(workflow, params, log)

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    NAMED WORKFLOW FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { CMGGPREPROCESSING } from "./workflows/cmgg-preprocessing"

//
// WORKFLOW: Run main CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing analysis pipeline
//
workflow CMGG_CMGGPREPROCESSING {
    CMGGPREPROCESSING ()
}

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

//
// WORKFLOW: Execute a single named workflow for the pipeline
// See: https://github.com/nf-core/rnaseq/issues/619
//
workflow {
    CMGG_CMGGPREPROCESSING ()
}

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