Nextstrain build for novel coronavirus SARS-CoV-2

Change Log

As of April 2021, we use major version numbers (e.g. v2) to reflect backward incompatible changes to the workflow that likely require you to update your Nextstrain installation. We also use this change log to document new features that maintain backward compatibility, indicating these features by the date they were added.

v5 (7 May 2021)

See the corresponding pull request for more details about this release.

Major changes

  • Drop support for old sequence/metadata inputs
  • Use nextalign for alignment instead of mafft

Minor changes

  • Drop unused haplotype status rule and script
  • Remove unused nucleotide mutation frequencies rule
  • Use augur distance for mutation counts

v4 (5 May 2021)

See the corresponding pull request for more details about changes in this release.

Major changes

  • Change the default build name from “global” to “default-build” and use a default subsampling scheme that selects all input sequences
  • Warn about duplicate sequences found when merging sequences from multiple inputs instead of throwing an error (set combine_sequences_for_subsampling: warn_about_duplicates: false in your configuration file to revert this behavior)

Features

  • Define a new subsampling scheme named all that selects all input sequences
  • Add a new top-level configuration parameter default_build_name to allow overriding new default name of “default-build”
  • Support compressed sequence inputs for alignment with mafft and nextalign (requires mafft upgrade)
  • Sanitize strain names in sequences and metadata from different sources (e.g., hCoV-19/ from GISAID or SARS-CoV-2/ from GenBank, etc.)

New features since last version update

  • 20 April 2021: Surface emerging lineage as a colorby. This replaces the rather stale color by “Emerging Clade” with a new color by “Emerging Lineage”. This focuses on PANGO lineages that are of interest triangulated by CoVariants, PANGO international lineage reports, CDC VUIs and VOCs and PHE VUIs and VOCs. The intention is for the listing at emerging_lineages.tsv to be updated frequently with new lineages added and no longer interesting lineages dropped. #609

  • 12 April 2021: Calculate current clade frequency and logistic growth rate across nodes in the phylogeny. This produces a new logistic_growth.json file and uses this file to add a coloring the final Auspice JSON. Implementation choices are discussed in PR #595.

  • 12 April 2021: Annotate Pangolin lineages per build in a pangolineages.json file and final Auspice JSON by adding run_pangolin: true to the top-level workflow config (builds.yaml). Note: this annotation only works when running the workflow with Snakemake’s --use-conda flag or if your environment has Pangolin installed. #593

v3 (12 April 2021)

  • Use Augur 11.2.0’s metadata-only output arguments to aggregate subsampled sequences and metadata #592
  • Use Augur 11.3.0’s io.py module to combine and deduplicate uncompressed or compressed sequences when handling multiple input datasets #592

v2 (9 April 2021)

This release reflects the state of the workflow when we instituted our workflow versioning system.

July 2020 Update

In order to make our repository more accessible for first-time users, and those who want to create their own customized build, we made a number of changes in July 2020. Here, we outline those changes, and also list ‘breaking changes’ that may effect advanced users who were already running their own builds.

You can check the lists below to see if there’s any action you could take to make updating to the latest version of this repository is smooth!

Summary of changes

The goal of this release is to make it easier for new users to get their own ncov build up and running. This consists of a new, extensive tutorial hosted on github pages; a simplified repository structure; and more didactic file names.

Summary of breaking changes:

  • All nextstrain-specific files now live under nextstrain_profiles
  • config is now named defaults
  • envs, rules and schemas now live under workflow

Additions and updates

  • README is updated
  • Adds in-depth tutorial to docs/ and accompanying github pages setup files
  • data/ now contains example data that should remain packaged with the repository
  • narratives/ now contains only a template_narrative.md for new users (not to worry – all finished Situation Reports are still hosted over in the nextstrain/narratives repo)
  • my_profiles now contains extensive example (formerly king-county) and example_advanced_customization (formerly swiss) profiles

File name changes

  • The main config.yaml file is now more precisely labeled as parameters.yaml
  • reference.gb > reference_seq.gb
  • ordering.tsv > color_ordering.tsv
  • config > defaults, with nextstrain-specific files (e.g., description.md) moved to nextstrain_profiles/nextstrain/
  • nextstrain-specific profiles labeled with nextstrain_*

Structural changes

To improve repo clarity and approachability for new users, the following files have been reorganized.

  • Workflow-related files now live in a workflow directory, rather than the top level
    • envs > workflow/envs
    • schemas > workflow/schemas
    • rules > workflow/snakemake_rules
  • Nextstrain-specific profiles now live under nextstrain_profiles

(Reiterated from last section because they’re important :)

  • config is now defaults, with nextstrain-specific files (e.g., description.md) moved to nextstrain_profiles/nextstrain/
  • config.yaml is now parameters.yaml

Breaking Changes

If you’ve got custom builds running and regularly pull from the repository, you should check here to see if any of the changes you’ve made might make the merge harder. Usually, just copying and renaming folders and/or files is enough to avoid too many merge conflicts!

First, you should check the file locations that have changed, above. If you reference any of these files specifically in your pipelines or profile, be sure to update those links!

Be sure to also check any links to files that were previously in profiles. For example, if you were referencing the cluster information in profiles/nextstrain-scicore/cluster.json for example) - we’ve now got two profiles folders - you’d find nextstrain-scicore in the nextstrain_profiles folder now.

If you modified the swiss, default, or king-county profiles, this may cause a merge conflict, as these folders have been renamed. To keep your builds as they are, we recommend copying these folders, and then after the merge, restoring the name you prefer.

We now have a data folder which comes with the repository and contains example build data. If you had previously created a data folder, this may cause a merge conflict - usually this can be easily resolved.

Developer Changes

For those who help run and maintain the Nextstrain.org builds, there’s a few changes that might be different from what you’re used to.

Just focusing on the files mostly accessed by the ‘build shepherds,’ here’s what’s good to know:

  • The config folder is now defaults
  • orderings.tsv is now color_orderings.tsv
  • rules/nextstrain_exports.smk (the rules that do the ‘finalizing’ of the builds) isnow workflow/snakemake_rules/export_for_nextstrain.smk

The ‘finishing builds’ commands are also slightly different because the profiles have moved - they’ll look familiar though! You can already find these changed commands in the export_for_nextstrain.smk file, but here they are as well:

# To update ordering/lat_longs after AWS download:
#   snakemake --touch --forceall --profile nextstrain_profiles/nextstrain
#   snakemake --profile nextstrain_profiles/nextstrain clean_export_regions
#   snakemake --profile nextstrain_profiles/nextstrain export_all_regions
# When done adjusting lat-longs & orders, remember to run
#   snakemake --profile nextstrain_profiles/nextstrain all_regions
# to produce the final Auspice files!