John Huddleston

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...

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....

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...

augur refine crashes when the root sequence is not included in the build

12

**Context** A common use case for ncov builds is to search for specific sequences in GISAID (e.g., for a specific emerging lineage, state, country, etc.) and create a build for...

Document color schemes

1

## Context At the beginning of the pandemic, [Trevor created a collection of color schemes that could scale to hundreds of categorical values](https://github.com/nextstrain/ncov/commit/f2e31be77adf4e51dcec500778f25dea70f89b81). [These color schemes](https://github.com/nextstrain/ncov/blob/master/defaults/color_schemes.tsv) were originally used to...

Build names do not allow "." characters

1

**Current Behavior** Users who want to create a build for a specific Pango lineage with a build name like "B.1.1.7" will get an obscure validation error from Snakemake because the...

Remove redundant include strains

1

## Description of proposed changes Removes older references from the list of strains to force include in analyses. We use the single Wuhan/Hu-1/2019 strains as the reference for alignment and...

**Current Behavior** The tutorial provides no recommendations about what kind of hardware is required to run the workflows. **Possible solution** Include a brief description of what kind of hardware can...

**Current Behavior** The current tutorial states that users can learn how to setup their own custom Nextstrain build in an hour, but the actual run-time of the tutorial is much...

## Context By default, augur frequencies sets a min and max date based on the collection dates present in the input data. [The ncov workflow explicitly hardcodes the `--min-date` and...