Mercurial > repos > fubar > egapx_runner
annotate nf/subworkflows/ncbi/gnomon-training-iteration/utilities.nf @ 8:1680e72e27be draft default tip
planemo upload for repository https://github.com/ncbi/egapx commit bdbe05027c2c40e217a2ff0c9e0556450c443e54
author | fubar |
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date | Mon, 05 Aug 2024 03:56:41 +0000 |
parents | d9c5c5b87fec |
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d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
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1 #!/usr/bin/env nextflow |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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2 nextflow.enable.dsl=2 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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3 // nextflow.preview.recursion=true |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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4 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
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5 include { chainer_wnode as chainer } from '../gnomon/chainer_wnode/main' |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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6 include { gnomon_wnode } from '../gnomon/gnomon_wnode/main' |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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7 include { gnomon_training } from '../gnomon/gnomon_training/main' |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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8 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
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9 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
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10 workflow gnomon_training_iteration { |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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11 take: |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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12 models_file |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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13 genome_asn |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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14 proteins_asn |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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15 chainer_alignments |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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16 chainer_evidence_denylist |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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17 chainer_gap_fill_allowlist |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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18 chainer_trusted_genes |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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19 chainer_scaffolds |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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20 gnomon_softmask_lds2 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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21 gnomon_softmask_lds2_source |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
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22 gnomon_scaffolds |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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23 max_intron |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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24 parameters |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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25 main: |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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26 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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27 chainer(chainer_alignments, models_file, chainer_evidence_denylist, chainer_gap_fill_allowlist, chainer_scaffolds, chainer_trusted_genes, genome_asn, proteins_asn, parameters.get('chainer', [:])) |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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28 gnomon_wnode(gnomon_scaffolds, chainer.out.chains, chainer.out.chains_slices, models_file, gnomon_softmask_lds2, gnomon_softmask_lds2_source, genome_asn, proteins_asn, parameters.get('gnomon', [:])) |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
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29 gnomon_training(genome_asn, gnomon_wnode.out.outputs, max_intron, parameters.get('gnomon_training', [:])) |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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30 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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31 emit: |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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32 hmm_params_file = gnomon_training.out.hmm_params_file |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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33 genome_asn = genome_asn |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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34 proteins_asn = proteins_asn |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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35 chainer_alignments = chainer_alignments |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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36 chainer_evidence_denylist = chainer_evidence_denylist |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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37 chainer_gap_fill_allowlist = chainer_gap_fill_allowlist |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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38 chainer_trusted_genes = chainer_trusted_genes |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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39 chainer_scaffolds = chainer_scaffolds |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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40 gnomon_softmask_lds2 = gnomon_softmask_lds2 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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41 gnomon_softmask_lds2_source = gnomon_softmask_lds2_source |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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42 gnomon_scaffolds = gnomon_scaffolds |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
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43 max_intron = max_intron |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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44 parameters = parameters |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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45 } |