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Update 2023 09 20 #124

Merged
merged 22 commits into from
Sep 21, 2023
Merged

Update 2023 09 20 #124

merged 22 commits into from
Sep 21, 2023

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erinyoung
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@erinyoung erinyoung commented Sep 20, 2023

Moderate update:

  • current-datasets is now set to false by default
  • changed datasets download to only download new genomes (does not download genomes from list)
    • This retires params.genome_references
  • updated fastani to 1.34
  • since fastani now allows *.gz as input, the included genomes are now separate compressed files
    • the 'decompression' process was removed
  • changed fastani_ref to accept a comma-delimited list of fasta files (or fasta.gz files) to be added to the fastani references
  • added fastani_ref_list to accept a file with a on each line for fasta files (or fasta.gz files) to be added to the fastani references

@erinyoung
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Resolves #122.

More genomes can probably be added in the future.

This was referenced Sep 20, 2023
@erinyoung erinyoung merged commit d9b10b5 into main Sep 21, 2023
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@erinyoung erinyoung deleted the update-2023-09-20 branch October 24, 2023 17:30
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