Update references to match RefSeq

[j23414]

Description of proposed changes

Switch to the RefSeq reference 'Josiah' for consistency.

Related issue(s)

• Addressing: Consistently pick a reference strain for all builds #22

Checklist

• Checks pass

[j23414]

Hmm, realizing that updating the references in phylogenetic triggers concurrent changes to segment references for ingest

• Separate curated data by L and S segments #12

[j23414]

I've moved the updating segment reference files to a separate issue. The main changes in this PR are from this slack thread:

1. Add Pinneo as explicit root
2. Update reference to be Josiah

Which results in the following trees:

• https://next.nextstrain.org/staging/lassa/l/rooted
• https://next.nextstrain.org/staging/lassa/s/rooted

[trvrb]

Thanks for putting this together @j23414. In the above I just passed in two tips instead to specify a clade to root to. This isn't perfect, but is a bit less funky than TreeTime's behavior of placing root exactly on the specified tip.

Also, I added include.txt to make sure to always include these strains.

You can see resulting output here:

• https://nextstrain.org/staging/lassa/l/rooted-with-outgroup-clade
• https://nextstrain.org/staging/lassa/s/rooted-with-outgroup-clade

[trvrb]

@j23414: Could you add MG812675 to the example data? This should make the CI complete.

[j23414]

Thanks @trvrb! I was wondering how to get a more reasonable root of the trees

I've updated the example data in 6405c92