diff nf/subworkflows/ncbi/gnomon-training-iteration/utilities.nf @ 0:d9c5c5b87fec draft

planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nf/subworkflows/ncbi/gnomon-training-iteration/utilities.nf	Sat Aug 03 11:16:53 2024 +0000
@@ -0,0 +1,45 @@
+#!/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
+}