Sync#21
Merged
Merged
Conversation
… data The tree shows some antibody escape scores from deep mutational scanning. This adds a link to the preprint describing that data source ([here](https://www.biorxiv.org/content/10.64898/2026.02.12.705519)) to README and description where before there was a dummy link. @rneher or @jameshadfield, can you review and merge?
…tation add citation to preprint for deep mutational scanning antibody escape data
In [this pull request](nextstrain#110), @rneher limited background sequences from recent builds to not include extinct preduplication lineages in order not to have the background sequences go back too far time. @victorlin noticed that a key part of this change was reverted in nextstrain#114 (see [here](https://github.com/nextstrain/rsv/pull/114/changes#r2835307384)); that reversion was incorrect. This pull request fixes that.
…ence-preduplication-filter-regression fix exclusion of preduplication sequence sequences from background
subrepo: subdir: "shared/vendored" merged: "37cf39c" upstream: origin: "https://github.com/nextstrain/shared" branch: "main" commit: "37cf39c" git-subrepo: version: "0.4.9" origin: "https://github.com/ingydotnet/git-subrepo" commit: "4f60dd7"
Useful for debugging.
augur filter has never taken a reference file as input, so my guess is this was originally copied by mistake.
Preparing to make changes to the config that would have broken this. It seems fine to hardcode along with the already hardcoded sample size.
This will make it easier to compare changes in the switch to augur subsample which will define all parameters in config.
This shouldn't rely on config from another rule.
Previously, logs were only captured for a few rules without a clear
mapping between log file and rule name.
This commit adds log and benchmark files to all rules with a consistent
name format of `{rule}_<wildcards>.txt` and usage of `exec` to capture
output.
<https://docs.nextstrain.org/en/latest/reference/snakemake-style-guide.html#log-standard-out-and-error-output-to-log-files-and-the-terminal>
<https://docs.nextstrain.org/en/latest/reference/snakemake-style-guide.html#always-use-the-benchmark-directive>
Improves readability of Snakemake console output. <https://docs.nextstrain.org/en/latest/reference/snakemake-style-guide.html#use-triple-quoted-command-definitions>
This allows Snakemake to show other critical details such as job id, rule name, input, output. <https://docs.nextstrain.org/en/latest/reference/snakemake-style-guide.html#avoid-the-message-rule-attribute>
This removes an unnecessary run of rule newreference with gene=genome. That had made an unnecessary file copy and conversion from GenBank to FASTA format. This is also more consistent with the existing get_alignment() function.
This removes an unnecessary run of rule newreference with gene=F-antibody-escape. build_name=F-antibody-escape now reuses the output files from gene=F.
All usage in the workflow specifies a gene.
This was added before .gitignore.
The previous behavior increased the chance of under-sampling by allowing
sequences that don't start with "{subtype}.D" to pass subsampling, only
to be later excluded. The new query approach turns it into a proper
pre-subsampling filter step, and also avoids an extra step in the
workflow.
"phylo: limit time-scoped builds to ancestor with G duplication" (af8a9b7) added a "1y" entry to resolutions under filter config, but not resolutions_to_run. I assume this was added by mistake.
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
4 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
Updating upstream fork
Related issue(s)
Checklist