main.nf

#!/usr/bin/env nextflow


nextflow.enable.dsl=2

// include non-process modules
include { help_message; version_message; complete_message; error_message; pipeline_start_message } from './modules/messages.nf'
include { default_params; check_params } from './modules/params_parser.nf'
include { help_or_version } from './modules/params_utilities.nf'

version = '1.0dev'

// setup default params
default_params = default_params()
// merge defaults with user params
merged_params = default_params + params

// help and version messages
help_or_version(merged_params, version)
final_params = check_params(merged_params)
// starting pipeline
pipeline_start_message(version, final_params)

// include processes and workflows 
include { NANOPORE } from './modules/workflow.nf' addParams(final_params)

workflow {

// Setup input Channel from Read path
        reads_ch = channel
                         .fromPath( final_params.reads )
                         .map { file -> tuple(file.simpleName, file) }
			 .ifEmpty { error "Cannot find any reads matching: ${final_params.reads}" }
			 
	NANOPORE(reads_ch)
}


workflow.onComplete {
    complete_message(final_params, workflow, version)
}

workflow.onError {
    error_message(workflow)
}