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scaffolding and reference selection based on ANI #528

Merged
merged 22 commits into from
Mar 25, 2024
Merged

scaffolding and reference selection based on ANI #528

merged 22 commits into from
Mar 25, 2024

Commits on Mar 20, 2024

  1. bump viral-assemble

    @dpark01
    dpark01 committed Mar 20, 2024
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  2. update to use new skani refsel code

    @dpark01
    dpark01 committed Mar 20, 2024
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  3. add more columns of output

    @dpark01
    dpark01 committed Mar 20, 2024
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  4. syntax fix

    @dpark01
    dpark01 committed Mar 20, 2024
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  5. fix call of fetch_row_from_tsv, add more workflow outputs

    @dpark01
    dpark01 committed Mar 20, 2024
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  6. defend more variables from whitespace in filenames; change task scaff… 

    …old reference selection to skani-based
    @dpark01
    dpark01 committed Mar 20, 2024
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  7. add more numeric outputs

    @dpark01
    dpark01 committed Mar 20, 2024
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  8. fix output ref

    @dpark01
    dpark01 committed Mar 20, 2024
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  9. fixes

    @dpark01
    dpark01 committed Mar 20, 2024
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  10. fixes

    @dpark01
    dpark01 committed Mar 20, 2024
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  11. drop unused inputs

    @dpark01
    dpark01 committed Mar 20, 2024
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  12. common input

    @dpark01
    dpark01 committed Mar 20, 2024
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  13. bump version of viral-assemble

    @dpark01
    dpark01 committed Mar 20, 2024
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  14. comment out one output variable

    @dpark01
    dpark01 committed Mar 20, 2024
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  15. fix some python

    @dpark01
    dpark01 committed Mar 20, 2024
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  16. bump viral-assemble docker

    @dpark01
    dpark01 committed Mar 20, 2024
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  17. some code cleanup and change workflow to guarantee unique ref fasta f… 

    …ilenames when non-unique taxids
    @dpark01
    dpark01 committed Mar 20, 2024
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  18. workaround some cromwell delocalization limitations

    @dpark01
    dpark01 committed Mar 20, 2024
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  19. oops, this is int not bool

    @dpark01
    dpark01 committed Mar 20, 2024
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  20. tweak output filename; bump viral-assemble docker

    @dpark01
    dpark01 committed Mar 20, 2024
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  21. accept multiple file inputs

    @dpark01
    dpark01 committed Mar 20, 2024
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Commits on Mar 21, 2024

  1. fallback to zeroes if assembly fails

    @dpark01
    dpark01 committed Mar 21, 2024
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