dogme.nf

#!/usr/bin/env nextflow


nextflow.enable.dsl=2

include { modWorkflow } from './nanoporeModule'

def getParamOrDefault(param, defaultValue) {
    if (param == null || param == 'null' || param == 'undefined' || !param) {
        return defaultValue
    } else {
        return param
    }
}

// Set the default value at the workflow level
def dogmeVersion = "0.88"


// Set the default value at the workflow level
def defaultModDir = "${launchDir}/doradoModels"

workflow {
    modDir = getParamOrDefault(params.modDir, defaultModDir)
    params.modDir = modDir
    println "dogme.nf modDir = ${modDir}"
    modWorkflow(dogmeVersion, 'sup,inosine_m6A,pseU,m5C', modDir)
}

// Define other processes similarly, ensuring they take `rnaMod` as an input
workflow.onComplete {
    // Execute cleanup command
    def cleanCommand = "rm -rf ${workflow.workDir}/*"
    println "Cleaning up work directory..."
    def process = cleanCommand.execute()
    process.waitFor()
    if (process.exitValue() == 0) {
        println "Work directory cleaned successfully."
    } else {
        println "Failed to clean work directory."
        println process.err.text
    }
}