ncov

ncov copied to clipboard

### Description of proposed changes: Update annotations up to August 9th, 2022. Let me know if I missed anything. Otherwise, I move to merge this Thursday morning, after the current...

j23414

## 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...

victorlin

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...

victorlin

Fix annotate metadata with numeric strains

1

## Description of proposed changes Fix annotate metadata with numeric strains by setting the dtype of the "strain" column in the sequence index to "string". ## Related issue(s) Fixes #948...

huddlej

Fix strain name sanitize logic

1

## Description of proposed changes Fixes three bugs. The first bug is in the sanitize logic for the workflow when run with data from GISAID's full FASTA and metadata downloads....

huddlej

Add parameter to enable overriding tree args

3

## Description of proposed changes Adds a configuration parameter to the workflow, `override_default_args`, in the `tree` section that allows users to toggle the corresponding new flag in `augur tree` on...

huddlej

**Context** I found S1 mutations a super useful coloring in the pre-Omicron days. Unfortunately, Omicron has so many S1 mutations now that new S1 mutations are no longer identifiable through...

corneliusroemer

I regularly get questions about how to reuse screenshots from Nextstrain (all so far about SC2). People don't seem to be finding the info at the bottom of Nextstrain.org. I...

emmahodcroft

The `files.exclude` parameter to the workflow only allows a single sequence exclusion file per build, which means that if I want to use a custom exclusion file in my custom...

sacundim

Memory resource definitions

2

## Description of proposed changes See commit messages. ## Related issue(s) Fixes #949 ## Testing - [ ] CI passes - [ ] Try to evaluate if the `mem_mb` as...

tsibley