diff nf/subworkflows/ncbi/orthology/main.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/orthology/main.nf	Sat Aug 03 11:16:53 2024 +0000
@@ -0,0 +1,43 @@
+#!/usr/bin/env nextflow
+// main nextflow script for EGAPx execution
+// route data to subworkflows
+
+nextflow.enable.dsl=2
+
+
+include { extract_products_from_models } from './extract_products_from_models/main'
+include { find_orthologs; fetch_ortholog_references; } from './find_orthologs/main'
+include { diamond_orthology } from './diamond_orthology/main'
+include { setup_genome; setup_proteins } from './../setup/main'
+include { get_swiss_prot_ids as get_prot_ref_ids } from '../shared/diamond/main'
+
+params.intermediate = false
+
+
+workflow orthology_plane {
+    take:
+        genome_asnb
+        gencoll_asn
+        models
+        annot_files
+        task_params     // task parameters for every task
+    main:
+        // Protein alignments
+        fetch_ortholog_references()
+        def (scaffolds_ref, gencoll_ref_asn, unpacked_genome_ref, genome_ref_asn, genome_ref_asnb) = setup_genome(fetch_ortholog_references.out.p14_genomic_fna, [], task_params.get('setup', [:]))
+        def (unpacked_proteins_ref, proteins_ref_asn, proteins_ref_asnb) = setup_proteins(fetch_ortholog_references.out.p14_protein_faa, task_params.get('setup', [:]))
+        def prot_ref_ids  = get_prot_ref_ids(proteins_ref_asnb)
+        //orthology plane
+        extract_products_from_models(annot_files, task_params.get('extract_products_from_models', [:]))
+        // reference side. 1) gencoll, annotation , genome and protein sequence --> asn cashe or LDS demon
+        
+        diamond_orthology(extract_products_from_models.out.prot_ids, prot_ref_ids , models, proteins_ref_asnb , task_params.get('diamond_orthology', [:]))
+
+        // input side 1) gencoll asn from setup, genome_asn from setup, protein from gnomon_wnode.out, annotation it is from annotbuilder annot_files or accepts_asn
+        find_orthologs( gencoll_asn,  gencoll_ref_asn,  annot_files, fetch_ortholog_references.out.annot_file, diamond_orthology.out.alignments, [],
+                        models, proteins_ref_asnb , genome_asnb, genome_ref_asnb ,  task_params.get('find_orthologs', [:]))
+
+    emit:
+        orthologs = find_orthologs.out.orthologs
+}
+