Pipeline fails at run_lineage_assignment when trying to use Nextclade version 3.0.0 about covid-19-signal

[jaleezyy]

Gotcha! I'll double-check that segment as I adjust for Nextclade v3 and its updated output (so while Nextclade 3 wouldn't run with this version regardless, you'd likely come across subsequent errors if it did).

ETA for patch: Thursday, January 25, 2024

[jaleezyy]

SIGNAL v1.6.3 brings Nextclade V3 support and should address the user-specified version install issues brought up when downgrading Nextclade.

Let me know if there are any other issues!

[jaleezyy]

Given the larger scale update between Nextclade 2 and 3, adjustments may take some time as I look into it. I presume specifying any version of Nextclade 2 (i.e., 2.12 or 2.14) within the config.yaml should allow for SIGNAL to run to completion in the meanwhile.

Thanks for your patience!

[PierreLyons]

Thanks for the quick response.

Unfortunately, downgrading via setting a different Nextclade version number in the config.yaml file doesn't seem to work for me. The pipeline ignores the version I put in, and instead the latest version of Nextclade will be installed and used, causing the same error.

I've managed to patch the issue by modifying the scripts/assign_lineage.py file like so:

1. comment out line 81
2. replace softrequest variable with software_ver in the if/else statement at lines 83, 84, 86, and 87.

This seems to allow the correct version of Nextclade to be run on my local setup.

Thanks