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jts / ncov-tools

Small collection of tools for performing quality control on coronavirus sequencing data and genomes
MIT License
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pangolin no longer has '-lv' flag #65

Closed dfornika closed 3 years ago

dfornika commented 3 years ago

This commit:

https://github.com/cov-lineages/pangolin/commit/d1ec05441be70c135e43e3be1b5b310154de8b3b#diff-60adb0b1d86889ec80ab00b2fe0ad9d0bedf1d3d250b52e8f56a63fba8533231

...removed the -lv flag that is used here:

https://github.com/jts/ncov-tools/blob/bf5aa2d878960fa436fd1ce82e72ee98dbc93223/workflow/rules/analysis.smk#L90

...which leads to pipeline failure.

jts commented 3 years ago

Thanks @dfornika for reporting and @rdeborja for the fix.