This PR has been extensively used and tested in production.
It contains two main changes:
Nextalign is used for translation
Pango lineages are assigned by running pangolin, in addition to the pango lineages that come from GISAID. So now there are three pango labels: a) GISAID, b) default, c) usher mode
Because pangolin required its own conda environment, I had to change how jobs are submitted to SLURM. Instead of using a fixed submit shell script, submission is handled by a python script wrapper that assembles the submit script from a template, adding conda activate nextstrain/pangolin based on the specific rule.
This PR has been extensively used and tested in production.
It contains two main changes:
Because pangolin required its own conda environment, I had to change how jobs are submitted to SLURM. Instead of using a fixed submit shell script, submission is handled by a python script wrapper that assembles the submit script from a template, adding
conda activate nextstrain/pangolinbased on the specific rule.