Mercurial > repos > fubar > egapx_runner

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

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planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
author fubar
date Sat, 03 Aug 2024 11:16:53 +0000
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0
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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1 #!/usr/bin/env nextflow
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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2 nextflow.enable.dsl=2
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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3
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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4 include { merge_params } from '../../utilities'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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5
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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6 workflow locus_link {
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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7 take:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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8 best_refseq_prot_hit
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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9 orthologs
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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10 annotation
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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11 gencoll_asn
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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12 gnomon_lds2_source
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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13 best_prot_hit
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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14 track_loci
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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15 comparisons
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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16 curr_prev_compare
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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17 gnomon_biotypes
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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18 lxr_data
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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19 proteins_asn
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20 name_from_ortholog
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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21 parameters // Map : extra parameter and parameter update
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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22 main:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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23 default_params = ""
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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24 effective_params = merge_params(default_params, parameters, 'locus_link')
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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25 run_locus_link(best_refseq_prot_hit, orthologs, annotation,
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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26 gencoll_asn, gnomon_lds2_source, best_prot_hit, track_loci, comparisons, curr_prev_compare,
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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27 gnomon_biotypes, lxr_data, proteins_asn, name_from_ortholog, default_params)
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28 emit:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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29 best_gnomon_prot_hit = run_locus_link.out.best_gnomon_prot_hit
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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30 best_refseq_prot_hit = run_locus_link.out.best_refseq_prot_hit
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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31 locustypes = run_locus_link.out.locustypes
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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32 locus = run_locus_link.out.locus
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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33 stats = run_locus_link.out.stats
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34 all = run_locus_link.out.all
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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35 }
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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36
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37
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38
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39 process run_locus_link {
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40 input:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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41 path best_refseq_prot_hit
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42 path orthologs
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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43 path annotation
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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44 path gencoll_asn
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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45 path gnomon_lds2_source, stageAs: 'genome/*'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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46 path best_prot_hit
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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47 path track_loci
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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48 path comparisons
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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49 path curr_prev_compare
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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50 path gnomon_biotypes
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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51 path lxr_data
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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52 path proteins_asn
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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53 path name_from_ortholog
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54 val parameters
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55 output:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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56 path ('output/best_gnomon_prot_hit.tsv'), emit: 'best_gnomon_prot_hit'
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57 path ('output/best_refseq_prot_hit.tsv'), emit: 'best_refseq_prot_hit'
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58 path ('output/locustypes.tsv'), emit: 'locustypes'
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59 path ('output/locus.lnk'), emit: 'locus'
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60 path ('output/stats.xml'), emit: 'stats'
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61 path ('output/*'), emit: 'all'
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62 script:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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63 """
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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64 mkdir -p output
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65 mkdir -p ./asncache/
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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66 prime_cache -cache ./asncache/ -ifmt asnb-seq-entry -i $proteins_asn -oseq-ids /dev/null -split-sequences
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67
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68 lds2_indexer -source genome/ -db LDS2
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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69 echo "${best_prot_hit.join('\n')}" > best_prot_hit.mft
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70 extract_prot_names -alns best_prot_hit.mft -nogenbank -o output/best_gnomon_prot_hit.tsv -asn-cache ./asncache/ -lds2 LDS2
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71 echo "${best_refseq_prot_hit.join('\n')}" > best_refseq_prot_hit.mft
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72 extract_prot_names -alns best_refseq_prot_hit.mft -nogenbank -o output/best_refseq_prot_hit.tsv -asn-cache ./asncache/ -lds2 LDS2
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73 echo "${annotation.join('\n')}" > annotation.mft
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74 echo "${curr_prev_compare.join('\n')}" > curr_prev_compare.mft
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75 echo "${comparisons.join('\n')}" > comparisons.mft
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76 str=""
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77 if [ ! -z "$orthologs" ]
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78 then
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79 str="\$str -orthologs $orthologs"
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80 fi
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81 if [ ! -z "$lxr_data" ]
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82 then
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83 str="\$str -lxr $lxr_data"
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84 else
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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85 touch lxr_data
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86 str="\$str -lxr lxr_data"
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87 fi
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88
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89 if [ ! -z "$track_loci" ]
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90 then
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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91 str="\$str -locus_track $track_loci"
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92 else
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93 touch track_loci
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94 str="\$str -locus_track track_loci"
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95 fi
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96 if [ ! -z "$name_from_ortholog" ]
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97 then
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98 str="\$str -name_from_ortholog_rpt $name_from_ortholog"
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99 else
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100 touch name_from_ortholog
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101 str="\$str -name_from_ortholog_rpt name_from_ortholog"
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102 fi
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103
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104 locus_type -no_acc_reserve -annots annotation.mft -gc $gencoll_asn -gnomon_biotype $gnomon_biotypes -o_stats output/stats.xml -o_locustypes output/locustypes.tsv -o_locus_lnk output/locus.lnk -annotcmp comparisons.mft -annotcmp_pb curr_prev_compare.mft \$str
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105 """
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106 stub:
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107 """
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108 mkdir -p output
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109 touch output/best_gnomon_prot_hit.tsv
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110 touch output/best_refseq_prot_hit.tsv
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111 touch output/locustypes.tsv
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112 touch output/locus.lnk
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113 touch output/stats.xml
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114 """
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115 }
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116