Victor Lin

Hello @Mustafa-Mohammed-58541, you can take a look at the [Contributing section in the repo README](https://github.com/nextstrain/ncov#contributing) as a start. Are you wanting to fix this issue specifically?

Assigning myself to fix the merge conflict with configuration.md, since I migrated that to [workflow-config-file.rst](https://github.com/nextstrain/ncov/blob/338e07e0c393f1288da3be61ebce6bca2d7d0ed4/docs/src/reference/workflow-config-file.rst). EDIT: done

@fanninpm that's great to hear! I'm not very involved in the TreeTime development, but I noticed that `--use-fft` was [added to the Nextstrain monkeypox workflow](https://github.com/nextstrain/monkeypox/commit/36da56e6201d3e742f42d3c2810b75fd365676c7) then [recently removed](https://github.com/nextstrain/monkeypox/commit/26c2fa1fbe8766c59685e2f611edabcfc98fdaf5). @corneliusroemer is...

Good point about the `grep`. Would it be equally beneficial to have the `sra=XXXX` for nucleotide summary files as well? That way it's more consistent.

I was able to do most of the finalizing work for this today. A few more unit tests that I'm figuring out how to implement since it doesn't seem like...

@ababaian done - moved all the test input files to `s3://serratus-public/test-data/benchmarker/`. Also added a `setup.sh` script to copy the files into `test/benchmarker/local/`. Using `local` for the folder name since it's...

A lot has happened since this was started. Is the benchmarker still needed? The last task is unit testing `msbar`, but it seems non-trivial. We could merge this PR in...

Oh ok! I also tried https://nextstrain.org/staging/ncov/gisaid/trial/victorlin-test-sqlite/global but makes sense why that doesn't work now. I'll make a PR to add `` and maybe a valid example URL too.

On naming: my only thought is **not** `augur transform`, since it looks/sounds similar to the existing but entirely different `augur translate`. I don't have strong thoughts on the other proposals...

Missing out on using @joverlee521's great work in other pathogen repos over naming issues is unfortunate. This feels like chicken and egg to me: I'd like to use these in...