We’re happy to announce the release of version 2 of the Public Health Bioinformatics repository!
This release simplifies the usage of the TheiaCoV workflows, introduces multiple new features, and standardizes variable names across all of our workflow offerings. These changes will make PHB workflows simpler to use and easier to learn, but will require adjustments from existing users who want to upgrade as several inputs and many outputs have changed.
This section lists the breaking changes between PHB v1.3.0 and PHB v2.0.0. For more details about each change in addition to non-breaking changes, please read the release notes .
Public Health Bioinformatics v2.0.0 Major Release Notes
It’s not necessary to upgrade to version 2.0.0, but we recommend it as several bug fixes and improvements have been made that will only be available in v2.0.0 and any subsequent versions.
If you’ve validated a previous version of PHB, feel free to continue using that. All previous versions will be available in perpetuity.
What it is: PHB v2 now incorporates all organism-specific parameters into the workflow by default. You no longer need to fill variables like vadr_opts, unless you want to, of course! You now need to only provide the organism name to make the workflow compatible with your organism (supported organisms: SARS-CoV-2, flu, mpox, HIV, WNV, RSV-A, RSV-B). All of the appropriate options are provided by default for each organism. This makes TheiaCoV more similar to TheiaProk, where organism-specific values are provided by default. User-provided inputs will always overwrite default values.
| Organism | Accepted values in “organism” parameter |
|---|---|
| SARS-CoV-2 | "sars-cov-2" , "SARS-CoV-2" |
| Influenza | "flu" , "influenza" , "Flu" , "Influenza" |
| Mpox | "MPXV" , "mpox" , "monkeypox" , "Monkeypox virus" , "Mpox" |
| HIV | "HIV" |
| WNV | "WNV" , "West Nile virus" , "wnv" |
| RSV-A | "rsv_a" , "rsv-a" , "RSV_A" , "RSV-A" |
| RSV-B | "rsv_b" , "rsv-b" , "RSV_B" , "RSV-B" |
What has changed: All provided input JSONs now contain only the dynamically changing resources, like the Pangolin docker image and Nextclade dataset tags.
What hasn’t changed: The default organism is still "sars-cov-2"
What to do: Nothing, or optionally, you can click on “Clear inputs” to remove all values in the inputs and refill only the values you want to specifically indicate. Note: when you click clear inputs, all fields are emptied.
What workflows are affected: All TheiaCoV workflows
These changes affect all workflows.
Over the creation of the PHB workflows, many different ways to say the same thing have appeared in our code. For example, genome_size was equivalent to est_genome_size which was equivalent to genome_len, etc. Having the same value represented by multiple different names was leading to confusion, and so we decided to standardize the language we’ve been using in all of our workflows to be the same. Below, you can see a table that details all of the language standardizations.
A lot of these changes are only visible in the code, and aren’t seen by the user on Terra. The separate databases below only list input and output changes (respectively) that are visible to users on Terra.
What to do: If you can’t find a variable that you used to be able to change or find, search for the old name in the following databases to see if its name has been changed.