Related Issues (20)
- Add lineage assignments to summary table HOT 1
- Pangolin Update changes probability column to conflict breaking assign_lineages.py HOT 1
- 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
- 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
- Pipeline fails at run_lineage_assignment when trying to use Nextclade version 3.0.0 HOT 4
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