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@erinyoung erinyoung released this 10 Dec 00:15
· 908 commits to master since this release
2.2.20211209
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Learn about vigilant mode.

In this release:

  • multifasta support
  • under the hood, vadr, pangolin, and nextclade are not run individually any longer - this is due to adding in multifasta support
  • nextclade prep process has been merged into the nextclade process - since nextclade is now only run once
    • a new parameter designating with nextclade dataset to use is introduced params.nextclade_dataset = 'sars-cov-2'
  • the algined fasta from nextclade can now be used to create a tree with iqtree
    • set params.msa = 'nextclade' when params.relatedness = true
  • a new script that uses pandas to combine nextclade, vadr, and pangolin results.
    • This changes the columns of the summary file (sorry!) in a new process named combine_results
  • using the quay.io/biocontainers/pandas:1.1.5 as the default container for the process summary and fasta_prep
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