Merged
Conversation
This is the minimum version required for Snakemake v9.6.2
Using the latest version available since we decided to just jump directly to version 9.
Selected plugins based on what we currently support for remote files in ncov <https://github.com/nextstrain/ncov/blob/41cf6470d3140963ff3e02c29241f80ae8ed9c33/workflow/snakemake_rules/remote_files.smk>
This was referenced Jul 3, 2025
No longer needed since we are removing Google Cloud support in ncov/remove_files <nextstrain/ncov#1180>
jameshadfield
approved these changes
Jul 13, 2025
Member
jameshadfield
left a comment
There was a problem hiding this comment.
Dockerfile looks good, and we've already been using this image to test a number of pathogen workflows. ncov CI is failing but will be resolved by nextstrain/ncov#1180, however that won't go in until after the runtime's released so perhaps we want to comment it out from CI for a while?
Contributor
Author
The pathogen-repo-ci tests do not block the release process of the Docker image, so I think leaving in the failing ncov test is fine for now (especially since the ncov PR should be merged soon after release). |
victorlin
approved these changes
Jul 21, 2025
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Description of proposed changes
Resolves #256
Upgrade to Snakemake v9.6.2
Checklist