#!/usr/bin/env nextflow
nextflow.enable.dsl=2
// nextflow.preview.recursion=true

include { chainer_wnode as chainer } from '../gnomon/chainer_wnode/main'
include { gnomon_wnode } from '../gnomon/gnomon_wnode/main'
include { gnomon_training } from '../gnomon/gnomon_training/main'


workflow gnomon_training_iteration {
    take:
        models_file
        genome_asn
        proteins_asn
        chainer_alignments
        chainer_evidence_denylist
        chainer_gap_fill_allowlist
        chainer_trusted_genes
        chainer_scaffolds
        gnomon_softmask_lds2
        gnomon_softmask_lds2_source
        gnomon_scaffolds
        max_intron
        parameters
    main:

        chainer(chainer_alignments, models_file, chainer_evidence_denylist, chainer_gap_fill_allowlist, chainer_scaffolds, chainer_trusted_genes, genome_asn, proteins_asn, parameters.get('chainer', [:]))
        gnomon_wnode(gnomon_scaffolds, chainer.out.chains, chainer.out.chains_slices, models_file, gnomon_softmask_lds2, gnomon_softmask_lds2_source, genome_asn, proteins_asn,  parameters.get('gnomon', [:]))
        gnomon_training(genome_asn, gnomon_wnode.out.outputs, max_intron, parameters.get('gnomon_training', [:]))

    emit:
        hmm_params_file = gnomon_training.out.hmm_params_file
        genome_asn = genome_asn
        proteins_asn = proteins_asn
        chainer_alignments = chainer_alignments
        chainer_evidence_denylist = chainer_evidence_denylist
        chainer_gap_fill_allowlist = chainer_gap_fill_allowlist
        chainer_trusted_genes = chainer_trusted_genes
        chainer_scaffolds = chainer_scaffolds
        gnomon_softmask_lds2 = gnomon_softmask_lds2
        gnomon_softmask_lds2_source = gnomon_softmask_lds2_source
        gnomon_scaffolds = gnomon_scaffolds
        max_intron = max_intron
        parameters = parameters
}