Heads up for when you update Nextclade to v1.10.0

[corneliusroemer]

I wanted to give you a small heads up. I found your repo through a quick code search, because it doesn't use --input-dataset for Nextclade run. Thus if you update to v1.10.0 (it was released yesterday), you will have to add a line. We recommend to use --input-dataset, but you can also add --input-virus-properties excplicitly.

See this issue for a detailed explanation: nextstrain/nextclade#703

You need to make a change like here: broadinstitute/viral-pipelines@97fd339

Sorry for the trouble.

[mattdmem]

Thank you for the heads up - we will update our code!

[corneliusroemer]

Patch version 1.10.1 comes with a more helpful error message in this use case.

https://github.com/nextstrain/nextclade/releases/tag/1.10.1

Here are notes that should help migrating:

Nextclade CLI 1.10.1 (2022-01-26)

[Fix] Improve error message when the virus properties file is missing #704

Since version 1.10.0 Nextclade CLI have introduced a new required input file, virus_properties.json and datasets and documentation were updated to match. However, users who don't use datasets might have encountered breakage due to a missing file: when running Nextclade CLI without either --input-dataset of --input-virus-properties flag provided, it would stop with an unclear error message. In this release we improve the error message, making sure that that explains the problem and offers a solution.

This does not affect Nextclade Web or Nextalign CLI.

In order to facilitate upgrades, for most users, we recommend to:

• download the latest dataset before each Nextclade CLI session (e.g. in the beginning of an automated workflow, or once you start a batch of experiments manually) using nextclade dataset get command
• use --input-dataset flag instead of individual --input-* flags for dataset files when issuing nextclade run command
• if necessary, override some of the individual input files using corresponding --input-* flags

[Fix] Add information about virus_properties.json or --input-virus-properties to changelog

In the excitement of bringing the new features, we forgot to mention virus_properties.json or --input-virus-properties in the changelog when Nextclade CLI 1.10.0 was released. We now added this information retroactively.

[mattdmem]

Fixed in an upcoming release.