Mercurial > repos > fubar > egapx_runner

annotate nf/subworkflows/ncbi/main.nf @ 0:d9c5c5b87fec draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
author fubar
date Sat, 03 Aug 2024 11:16:53 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
1 #!/usr/bin/env nextflow
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
2 // main nextflow script for EGAPx execution
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
3 // route data to subworkflows
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
4
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
5 nextflow.enable.dsl=2
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
6
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
7 include { rnaseq_short_plane } from './rnaseq_short/main'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
8 include { target_proteins_plane } from './target_proteins/main'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
9 include { gnomon_plane; post_gnomon_plane } from './gnomon/main'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
10 include { orthology_plane } from './orthology/main'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
11 include { setup_genome; setup_proteins } from './setup/main'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
12 include { annot_builder } from './default/annot_builder/main'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
13 include { annotwriter } from './default/annotwriter/main'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
14
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
15
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
16 params.intermediate = false
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
17 params.use_orthology = false
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
18 params.use_post_gnomon = false
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
19
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
20
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
21 workflow egapx {
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
22 take:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
23 genome // path to genome
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
24 proteins // path to proteins, optional
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
25
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
26 // Alternative groups of parameters, one of them should be set
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
27 // reads_query - SRA query in the form accepted by NCBI
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
28 // reads_ids - list of SRA IDs
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
29 // reads, reads_metadata - path to reads accompanied by metadata
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
30 reads_query // SRA query
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
31 reads_ids // list of SRA IDs
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
32 reads // path to reads
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
33 reads_metadata // path to reads metadata 13 tab-delimited fields, 1-st - SRA ID, 3-rd paired or unpaired, everything else - not used, but must be present
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
34 // 4, 5, 13 - numbers, 5 - non zero number
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
35
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
36 organelles // path to organelle list
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
37 // Alternative parameters, one of them should be set
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
38 // tax_id - NCBI tax id of the closest taxon to the genome
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
39 // hmm_params - HMM parameters
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
40 tax_id // NCBI tax id of the closest taxon to the genome
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
41 hmm_params // HMM parameters
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
42 hmm_taxid // NCBI tax id of the HMM
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
43 //
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
44 softmask // softmask for GNOMON, optional
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
45 //
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
46 max_intron // max intron length
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
47 genome_size_threshold // the threshold for calculating actual max intron length
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
48 task_params // task parameters for every task
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
49 main:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
50 print "workflow.container: ${workflow.container}"
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
51
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
52 def setup_genome_params = task_params.get('setup', [:])
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
53 setup_genome_params['max_intron'] = max_intron
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
54 setup_genome_params['genome_size_threshold'] = genome_size_threshold
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
55 def (scaffolds, gencoll_asn, unpacked_genome, genome_asn, genome_asnb, eff_max_intron) = setup_genome(genome, organelles, setup_genome_params)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
56
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
57 // Protein alignments
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
58 def protein_alignments = []
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
59 def unpacked_proteins
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
60 def proteins_asn = []
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
61 def proteins_asnb = []
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
62 if (proteins) {
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
63 // miniprot plane
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
64 (unpacked_proteins, proteins_asn) = setup_proteins(proteins, task_params.get('setup', [:]))
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
65 target_proteins_plane(unpacked_genome, genome_asn, gencoll_asn, unpacked_proteins, proteins_asn, eff_max_intron, task_params)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
66 protein_alignments = target_proteins_plane.out.protein_alignments
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
67 }
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
68
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
69 // RNASeq short alignments
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
70 def rnaseq_alignments = []
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
71 if (reads_query || reads_ids || reads) {
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
72 rnaseq_short_plane(genome_asn, scaffolds, unpacked_genome, reads_query, reads_ids, reads, reads_metadata, organelles, tax_id, eff_max_intron, task_params)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
73 rnaseq_alignments = rnaseq_short_plane.out.rnaseq_alignments
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
74 }
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
75
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
76 // Combine RNASeq and protein alignments
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
77 def alignments
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
78 if (proteins && (reads_query || reads_ids || reads)) [
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
79 alignments = rnaseq_alignments.combine(protein_alignments)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
80 ] else if (proteins) {
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
81 alignments = protein_alignments
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
82 } else {
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
83 alignments = rnaseq_alignments
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
84 }
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
85
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
86 // GNOMON
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
87
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
88 def gnomon_models = []
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
89 def effective_hmm
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
90 gnomon_plane(genome_asn, scaffolds, gencoll_asn, proteins_asn, alignments, tax_id, hmm_params, hmm_taxid, softmask, eff_max_intron, task_params)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
91 gnomon_models = gnomon_plane.out.gnomon_models
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
92
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
93
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
94 // outputs
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
95 annot_builder(gencoll_asn, gnomon_models, genome_asn, task_params.get('annot_builder', [:]))
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
96 def accept_annot_file = annot_builder.out.accept_ftable_annot
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
97 def annot_files = annot_builder.out.annot_files
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
98
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
99 if (params.use_orthology) {
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
100 // ORTHOLOGY
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
101 orthology_plane(genome_asnb, gencoll_asn, gnomon_models, annot_files, task_params)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
102 def orthologs = orthology_plane.out.orthologs
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
103 if (params.use_post_gnomon) {
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
104 //POST GNOMON
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
105 post_gnomon_plane(gnomon_models, gencoll_asn, orthologs, tax_id, task_params)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
106 }
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
107 }
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
108
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
109 annotwriter(accept_annot_file, [:])
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
110 annotwriter.out.annoted_file
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
111
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
112 emit:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
113 out_files = annotwriter.out.annoted_file
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
114 annot_builder_output = annot_builder.out.outputs
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
115 // locus = post_gnomon_plane.out.locus
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff changeset
116 }