main.nf

#!/usr/bin/env nextflow
/*
========================================================================================
                         nf-core/viralrecon
========================================================================================
 nf-core/viralrecon Analysis Pipeline.
 #### Homepage / Documentation
 https://github.com/nf-core/viralrecon
----------------------------------------------------------------------------------------
*/

nextflow.enable.dsl = 2

////////////////////////////////////////////////////
/* --               PRINT HELP                 -- */
////////////////////////////////////////////////////

def json_schema = "$projectDir/nextflow_schema.json"
if (params.help) {
    def command = "nextflow run nf-core/viralrecon --input samplesheet.csv --genome 'MN908947.3' -profile docker"
    log.info Schema.params_help(workflow, params, json_schema, command)
    exit 0
}

////////////////////////////////////////////////////
/* --        GENOME PARAMETER VALUES           -- */
////////////////////////////////////////////////////

params.fasta         = Checks.get_genome_attribute(params, 'fasta')
params.gff           = Checks.get_genome_attribute(params, 'gff')
params.bowtie2_index = Checks.get_genome_attribute(params, 'bowtie2')

////////////////////////////////////////////////////
/* --         PRINT PARAMETER SUMMARY          -- */
////////////////////////////////////////////////////

def summary_params = Schema.params_summary_map(workflow, params, json_schema)
log.info Schema.params_summary_log(workflow, params, json_schema)

////////////////////////////////////////////////////
/* --          PARAMETER CHECKS                -- */
////////////////////////////////////////////////////

// Check that conda channels are set-up correctly
if (params.enable_conda) {
    Checks.check_conda_channels(log)
}

// Check AWS batch settings
Checks.aws_batch(workflow, params)

// Check the hostnames against configured profiles
Checks.hostname(workflow, params, log)

// Check sequencing platform
def platformList = ['illumina', 'nanopore']
if (!params.public_data_ids && !platformList.contains(params.platform)) {
    exit 1, "Invalid platform option: ${params.platform}. Valid options: ${platformList.join(', ')}"
}

////////////////////////////////////////////////////
/* --           RUN MAIN WORKFLOW              -- */
////////////////////////////////////////////////////

workflow {
    /*
     * SUBWORKFLOW: Get SRA run information for public database ids, download and md5sum check FastQ files, auto-create samplesheet
     */
    if (params.public_data_ids) {
        include { SRA_DOWNLOAD } from './workflows/sra_download' addParams( summary_params: summary_params )
        SRA_DOWNLOAD ()
    
    /*
     * SUBWORKFLOW: Variant analysis for Illumina data
     */
    } else if (params.platform == 'illumina') {
        include { ILLUMINA } from './workflows/illumina' addParams( summary_params: summary_params )
        ILLUMINA ()
    }

////////////////////////////////////////////////////
/* --                  THE END                 -- */
////////////////////////////////////////////////////