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annotate nf/subworkflows/ncbi/gnomon-training-iteration/main.nf @ 5:6effccc966d0 draft

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planemo upload for repository https://github.com/ncbi/egapx commit 9e59da535540cb4d5c1c412bb2b0969744dfb0b0
author fubar
date Sun, 04 Aug 2024 01:59:37 +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 nextflow.enable.dsl=2
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3 //nextflow.preview.recursion=true
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4
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5
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6 include { gnomon_training_iteration; gnomon_training_iteration as gnomon_training_iteration2;
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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7 gnomon_training_iteration as gnomon_training_iteration3; gnomon_training_iteration as gnomon_training_iteration4 } from './utilities'
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8
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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9
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10 workflow gnomon_training_iterations {
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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11 take:
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12 models_file
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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13 genome_asn
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14 proteins_asn
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15 chainer_alignments
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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16 chainer_evidence_denylist
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17 chainer_gap_fill_allowlist
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18 chainer_trusted_genes
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19 chainer_scaffolds
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20 gnomon_softmask_lds2
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21 gnomon_softmask_lds2_source
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22 gnomon_scaffolds
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23 max_intron
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24 parameters
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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25 main:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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26 gnomon_training_iteration(models_file, genome_asn, proteins_asn ,chainer_alignments,chainer_evidence_denylist,chainer_gap_fill_allowlist,
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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27 chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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28 gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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29 gnomon_training_iteration2(gnomon_training_iteration.out.hmm_params_file, genome_asn, proteins_asn ,chainer_alignments,
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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30 chainer_evidence_denylist,chainer_gap_fill_allowlist, chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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31 gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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32 gnomon_training_iteration3(gnomon_training_iteration2.out.hmm_params_file, genome_asn, proteins_asn ,chainer_alignments,
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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33 chainer_evidence_denylist,chainer_gap_fill_allowlist, chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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34 gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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35 gnomon_training_iteration4(gnomon_training_iteration3.out.hmm_params_file, genome_asn, proteins_asn ,chainer_alignments,
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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36 chainer_evidence_denylist,chainer_gap_fill_allowlist, chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
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37 gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
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38
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39 emit:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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40 hmm_params_file = gnomon_training_iteration4.out.hmm_params_file
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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41 }
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42
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43 workflow gnomon_no_training {
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44 take:
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45 hmm
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46 main:
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47 process_no_training(hmm)
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48 emit:
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49 hmm_params_file = process_no_training.out.file
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50 }
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51
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52 process process_no_training
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53 {
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54 input:
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55 val hmm
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56 output:
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57 path "*.params" , emit: 'file'
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58 script:
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59 """
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60 curl -O ${hmm}
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61 """
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62 stub:
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63 """
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64 touch hmm.params
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65 """
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66 }
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67
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68
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69 /*
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70
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71 //experimental (preview.recursion)
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72 // to be used in the future
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73 workflow gnomon_training_iterations {
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74 take:
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75 models_file
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76 genome_asn
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77 proteins_asn
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78 chainer_alignments
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79 chainer_evidence_denylist
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80 chainer_gap_fill_allowlist
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81 chainer_trusted_genes
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82 chainer_scaffolds
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83 gnomon_softmask_lds2
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84 gnomon_softmask_lds2_source
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85 gnomon_scaffolds
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86 max_intron
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87 parameters
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88 main:
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89 gnomon_training_iteration
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90 .recurse(models_file, genome_asn, proteins_asn ,chainer_alignments,chainer_evidence_denylist,chainer_gap_fill_allowlist,
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91 chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
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92 gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
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93 .times(4)
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94 emit:
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95 hmm_params_file = gnomon_training_iteration.out.hmm_params_file
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96 }
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d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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