[heads up] Nextclade v2.0

[fanninpm]

Today, Nextclade v2.0 was released, with a lot of improvements (especially in performance). However, the new version contains a couple of breaking changes that may break your workflow…

• The input FASTA argument is now a positional argument, and it's now possible to specify more than one input FASTA file (no more need to cat them together!).
• The --output-dir flag has now been superseded by the --output-all flag. (Also, the --output-{json,csv,tsv,tree} flags have become redundant if you only use the default names for those output files. Here is the file that specifies the CLI flags and the default output file names.)

Best of luck with the new version!

[erinyoung]

Thank you for letting me know! I had this in my calendar, but then didn't get to it. I'll hopefully have a new version and update by the end of the week this week.

[erinyoung]

Thank you again for this issue. I updated the nextclade and nextalign processes and it appears everything is working fine again in #102