Victor Lin

`gh release create`: Allow tag names for `--target`

6

### Describe the feature or problem you’d like to solve I want to create a release only if the tag exists (do not want auto tag creation with `gh release...

Add git switch suggestion in checkout error hint

5

It would be nice suggest a `git switch` command when facing the error from running `git switch ` where `` matches multiple remote tracking branches. --- Thanks for taking the...

## Description of proposed changes Add `TIME_SPAN` and valid example URLs to rebuild outputs. ## Related issue(s) - Fixes #990 ## Testing - [ ] run rebuild GH workflows and...

URL preview from rebuild-gisaid.yml output does not work

2

**Current Behavior** I ran [rebuild-gisaid.yml](https://github.com/nextstrain/ncov/blob/338e07e0c393f1288da3be61ebce6bca2d7d0ed4/.github/workflows/rebuild-gisaid.yml) to test this workflow running with `augur filter --engine sqlite`, a feature being developed in nextstrain/augur#854. I see that the Batch job has succeeded, and...

## Description of proposed changes Expanding some thoughts from https://github.com/nextstrain/ncov/pull/894#discussion_r843096418 and [Slack thread](https://bedfordlab.slack.com/archives/C02Q4Q5S85A/p1646334170382399). This is intended to be more of a discussion, but created as a draft PR to have...

- [ ] Document predefined subsampling schemes `all`, `region`, `region_global`, `region_grouped_by_country`, `country`, `division`, `location` _from https://github.com/nextstrain/ncov/pull/894#discussion_r832704630_ - [ ] prohibit certain suffixes in `builds:` entry names _from https://github.com/nextstrain/ncov/pull/896#discussion_r836882802_ 1. Update...

Summary file version inconsistencies

3

Examples for ERR2756788. Original summary header line [[S3 link](https://s3.amazonaws.com/lovelywater/summary/ERR2756788.summary)]: ``` SUMZER_COMMENT=sra=ERR2756788,genome=cov3ma,date=200607-01:47; ``` New summary header line [[S3 link](https://s3.amazonaws.com/lovelywater/summary2/ERR2756788.summary)]: ``` readlength=150;SUMZER_COMMENT=sra=ERR2756788,genome=cov3ma,version=200818,date=200817-21:05; ``` New psummary contents [[S3 link](https://s3.amazonaws.com/lovelywater/psummary/ERR2756788.psummary)]: ``` sra=ERR2756788;SUMZER_COMMENT=sra=ERR2756788,genome=protref5,date=200831-02:23,type=protein;totalalns=77449;readlength=141;truncated=no; sra=ERR2756788;famcvg=AAUWAWAAUAAAWWAAOAAWAAAAO;fam=Coronaviridae;score=100;pctid=71;alns=16477;avgcols=47; sra=ERR2756788;famcvg=auwa_aoa_awwwu_aoowmmamo_;fam=Dicistroviridae;score=100;pctid=68;alns=663;avgcols=47;...

Update benchmarking script with new CLI

7

Opening this PR to track progress for #27. Keeping as draft until ready. TODO: - split into 2 scripts - `cov_benchmark.py` - [x] design high-level CLI - [x] implement simulation...

docs: broken image links on QC page

4

Example: https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/07-quality-control.html https://github.com/nextstrain/nextclade/blob/ccf2a0429e239e29a20dd4da1148b908ed2d8515/docs/user/algorithm/07-quality-control.md?plain=1#L51 gets rendered as: ```html ``` and the absolute path is not valid in the context of docs.nextstrain.org/projects/nextclade. --- However, this [Nextclade Web](https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-web.html) image https://github.com/nextstrain/nextclade/blob/ccf2a0429e239e29a20dd4da1148b908ed2d8515/docs/user/nextclade-web.md?plain=1#L21 gets rendered with...

Error when metadata to `get_numerical_dates()` is not a pandas DataFrame

1

### Description of proposed changes See commit messages and #1025. ### Related issue(s) - Fixes #1025 ### Testing - [x] Added 84a4b0397e90c80947a48ab9f1e811382933f323 which fails, then fixed it with the following...