Comments (4)
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
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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!
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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!
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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:
- comment out line 81
- 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
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Related Issues (20)
- Lineage Assignment Failure preventing postprocess HOT 1
- Switch remaining default output to freebayes vs iVar
- Primer Scheme Correction HOT 1
- Revisit output layout
- Add Continuous Integration tests and linting
- Fix containerization
- Convert rules for wrapped tools to official wrapper
- support for pangolin v3.0.1 HOT 2
- ValidationError: 'sample' is a required property HOT 2
- Incorporate scorpio calls into report
- Galaxy workflow?
- Support IonTorrent .bam input
- Cleanup
- RuleException in line 549 of: filepath/Snakefile: 'Params' object has no attribute 'unlabelled_output_dir' HOT 2
- Update npm nextclade to the proper nextclade_cli HOT 1
- SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly HOT 2
- gunzip silently fails when running get_data_dependencies.sh HOT 1
- Dependency issues on new install with ivar conda environment HOT 5
- Artic-ncov2019 primer scheme V5.3.2 HOT 3
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