hap.nf

//load in help function
File helppages_class_file = new File("./src/Helppages.groovy");
Class HelppagesClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(helppages_class_file);
GroovyObject help = (GroovyObject) HelppagesClass.newInstance();

if (params.help) { exit 0, help.helpHap(workflow.manifest.version, params) }

// include modules - here, modules are single processes
//include { AMPLISIM }          from './modules/amplisim/main.nf'
include { MASON_SIMULATOR }     from './modules/mason/simulator/main.nf'
include { MASON_VARIATOR }      from './modules/mason/variator/main.nf'
//include { NANOSIM }           from './modules/nanosim/main.nf'
include { PBSIM }               from './modules/pbsim/main.nf'
//include { NORM_VCF }          from './subworkflows/norm_vcf/main.nf'
include { SAMTOOLS_FAIDX }      from './modules/samtools/faidx/main.nf'
include { MINIMAP2SAMTOOLS }    from './modules/minimap/main.nf'
include { N_STRETCHES}          from './modules/nstretches/main.nf'


workflow{
    // --------------
    // Input channels
    // --------------
    ch_ids      = Channel.of(1..params.n)
    ch_ref      = Channel.value("$baseDir/" + params.reference)

    // --------------
    // Prepare reference
    // --------------
    ch_ref_idx  = SAMTOOLS_FAIDX(ch_ref)

    if (params.report_nstretches){
        N_STRETCHES(ch_ref)
    }

    // --------------
    // Generate samples (haplotype FASTA + VCF)
    // --------------
    (ch_haplos,ch_vcf) = MASON_VARIATOR(ch_ids,ch_ref,ch_ref_idx)

    // Normalize, sort and index the VCF files
    //NORM_VCF(ch_vcf,ch_ref)

    // --------------
    // Generate reads
    // --------------
    if (params.read_type == 'ngs'){
        ch_vcf
            .map { it -> tuple(it.toString().split('/')[-1].tokenize('_')[1].replaceFirst('hap', '').replaceFirst('\\.vcf', '').toInteger(), file(it)) }
            .set {ch_sample_vcf_map}

        MASON_SIMULATOR(ch_sample_vcf_map,ch_ref,ch_ref_idx)
    }
    else if (params.read_type == 'ont'){
        ch_haplos
            .map { it -> tuple(it.toString().split('/')[-1].tokenize('_')[1].replaceFirst('hap', '').replaceFirst('\\.fasta', '').toInteger(), file(it)) }
            .set {ch_sample_haplos_map}

        ch_fastqs = PBSIM(ch_sample_haplos_map)

        MINIMAP2SAMTOOLS(ch_fastqs,ch_ref,ch_ref_idx)
    }


}