John Huddleston

Raise a meaningful error when "focus" priorities field in subsampling rule isn't a valid key

2

**Current Behavior** If a subsampling rule defines a priorities entry with a `focus` key that does not exist in the subsampling rule, the user will see an error like this:...

Validate input files from build configuration and provide helpful feedback

2

## Context We require users to define at least one entry in the `inputs` entry of their builds configuration. The syntax for these inputs can be confusing leading to common...

Set recommended minimum branch length for IQ-TREE

4

## Context As part of [a separate issue related to IQ-TREE and this workflow](https://github.com/iqtree/iqtree2/issues/40), we learned that the minimum branch length for IQ-TREE with SARS-CoV-2 data should be much lower—`-blmin...

**Current Behavior** Epiweek annotations are included in the main Nextstrain builds (GISAID and open), but these annotations only appear in the "Color By" dropdown as "epiweek" and they do not...

**Context** [The diagram overview of the ncov workflow](https://docs.nextstrain.org/projects/ncov/en/latest/analysis/orientation-workflow.html#overview-of-a-nextstrain-build-analysis-workflow) is outdated. We originally implemented this diagram as a vector graphic in the commerical tool Sketch. **Description** Update the ncov workflow diagram...

Exit with an error when user requests an undefined subsampling scheme

2

**Current Behavior** If a user requests an undefined subsampling scheme (that sounds logical to them as a scheme that _should_ exist like "state" or "county"), [the current workflow will print...

Left join multiple metadata files for the same named input

1

**Context** A common use case for the ncov workflow is for users to download GISAID data for a specific analysis (e.g., a state-focused build) and combine other existing metadata they...

## Description of proposed changes Uses Jaccard distance between sets of amino acid substitutions annotates in GISAID metadata as an alternative to the SNP-based proximity calculation. This approach does not...

## Context This workflow is (or can be) complicated depending on the inputs and subsampling schemes defined in a builds configuration. Users without substantial Snakemake and/or shell experience may not...

## Description of proposed changes Adds an updated figure of the full workflow (generated by Snakemake) and starts to revise the introductory text.