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planemo upload for repository https://github.com/ncbi/egapx commit bdbe05027c2c40e217a2ff0c9e0556450c443e54
author fubar
date Mon, 05 Aug 2024 03:56:41 +0000
parents d9c5c5b87fec
children
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d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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1 #!/usr/bin/env nextflow
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2 // main nextflow script for EGAPx execution
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3 // route data to subworkflows
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5 nextflow.enable.dsl=2
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7 include { rnaseq_short_plane } from './rnaseq_short/main'
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8 include { target_proteins_plane } from './target_proteins/main'
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9 include { gnomon_plane; post_gnomon_plane } from './gnomon/main'
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10 include { orthology_plane } from './orthology/main'
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11 include { setup_genome; setup_proteins } from './setup/main'
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12 include { annot_builder } from './default/annot_builder/main'
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13 include { annotwriter } from './default/annotwriter/main'
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16 params.intermediate = false
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17 params.use_orthology = false
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18 params.use_post_gnomon = false
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21 workflow egapx {
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22 take:
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23 genome // path to genome
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24 proteins // path to proteins, optional
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26 // Alternative groups of parameters, one of them should be set
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27 // reads_query - SRA query in the form accepted by NCBI
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28 // reads_ids - list of SRA IDs
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29 // reads, reads_metadata - path to reads accompanied by metadata
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30 reads_query // SRA query
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31 reads_ids // list of SRA IDs
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32 reads // path to reads
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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
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34 // 4, 5, 13 - numbers, 5 - non zero number
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36 organelles // path to organelle list
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37 // Alternative parameters, one of them should be set
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38 // tax_id - NCBI tax id of the closest taxon to the genome
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39 // hmm_params - HMM parameters
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40 tax_id // NCBI tax id of the closest taxon to the genome
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41 hmm_params // HMM parameters
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42 hmm_taxid // NCBI tax id of the HMM
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43 //
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44 softmask // softmask for GNOMON, optional
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45 //
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46 max_intron // max intron length
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47 genome_size_threshold // the threshold for calculating actual max intron length
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48 task_params // task parameters for every task
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49 main:
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50 print "workflow.container: ${workflow.container}"
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51
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52 def setup_genome_params = task_params.get('setup', [:])
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53 setup_genome_params['max_intron'] = max_intron
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54 setup_genome_params['genome_size_threshold'] = genome_size_threshold
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55 def (scaffolds, gencoll_asn, unpacked_genome, genome_asn, genome_asnb, eff_max_intron) = setup_genome(genome, organelles, setup_genome_params)
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56
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57 // Protein alignments
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58 def protein_alignments = []
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59 def unpacked_proteins
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60 def proteins_asn = []
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61 def proteins_asnb = []
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62 if (proteins) {
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63 // miniprot plane
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64 (unpacked_proteins, proteins_asn) = setup_proteins(proteins, task_params.get('setup', [:]))
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65 target_proteins_plane(unpacked_genome, genome_asn, gencoll_asn, unpacked_proteins, proteins_asn, eff_max_intron, task_params)
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66 protein_alignments = target_proteins_plane.out.protein_alignments
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67 }
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68
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69 // RNASeq short alignments
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70 def rnaseq_alignments = []
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71 if (reads_query || reads_ids || reads) {
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72 rnaseq_short_plane(genome_asn, scaffolds, unpacked_genome, reads_query, reads_ids, reads, reads_metadata, organelles, tax_id, eff_max_intron, task_params)
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73 rnaseq_alignments = rnaseq_short_plane.out.rnaseq_alignments
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74 }
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75
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76 // Combine RNASeq and protein alignments
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77 def alignments
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78 if (proteins && (reads_query || reads_ids || reads)) [
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79 alignments = rnaseq_alignments.combine(protein_alignments)
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80 ] else if (proteins) {
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81 alignments = protein_alignments
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82 } else {
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83 alignments = rnaseq_alignments
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84 }
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85
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86 // GNOMON
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87
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88 def gnomon_models = []
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89 def effective_hmm
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90 gnomon_plane(genome_asn, scaffolds, gencoll_asn, proteins_asn, alignments, tax_id, hmm_params, hmm_taxid, softmask, eff_max_intron, task_params)
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91 gnomon_models = gnomon_plane.out.gnomon_models
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92
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93
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94 // outputs
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95 annot_builder(gencoll_asn, gnomon_models, genome_asn, task_params.get('annot_builder', [:]))
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96 def accept_annot_file = annot_builder.out.accept_ftable_annot
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97 def annot_files = annot_builder.out.annot_files
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98
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99 if (params.use_orthology) {
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100 // ORTHOLOGY
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101 orthology_plane(genome_asnb, gencoll_asn, gnomon_models, annot_files, task_params)
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102 def orthologs = orthology_plane.out.orthologs
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103 if (params.use_post_gnomon) {
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104 //POST GNOMON
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105 post_gnomon_plane(gnomon_models, gencoll_asn, orthologs, tax_id, task_params)
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106 }
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107 }
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108
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109 annotwriter(accept_annot_file, [:])
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110 annotwriter.out.annoted_file
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111
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112 emit:
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113 out_files = annotwriter.out.annoted_file
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114 annot_builder_output = annot_builder.out.outputs
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115 // locus = post_gnomon_plane.out.locus
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116 }