Remove orphan rules find_clusters and extract_meta#1209
Open
trvrb wants to merge 2 commits into
Open
Conversation
Both rules produce outputs that are never consumed by any other rule or build target, so they never run in practice. - find_clusters (main_workflow.smk) + scripts/find_clusters.py + the cluster: config block in defaults/parameters.yaml that only it read. Its clusters.tsv output has no downstream consumer. - extract_meta (export_for_nextstrain.smk); its extracted_metadata.tsv output has no downstream consumer. The manual maintenance rules clean_export_regions / export_all_regions are kept deliberately: they are a documented in-file procedure (re-curating lat_longs and color_ordering after an AWS data download via scripts/check_missing_locations.py) that operates on still-active files. A dry-run of the CI profile is unchanged (37-job DAG, no errors). Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
This was referenced Jun 27, 2026
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Second in the pandemic-era cruft cleanup series (after #1208).
Motivation
A couple of rules produce outputs that nothing downstream consumes, so they never run as part of any build. Removing them shrinks the workflow with no behavior change.
What's removed
find_clusters(main_workflow.smk) +scripts/find_clusters.py+ thecluster:block indefaults/parameters.yamlthat only this rule read. Itsclusters.tsvoutput has no downstream consumer.extract_meta(export_for_nextstrain.smk); itsextracted_metadata.tsvoutput has no downstream consumer.Deliberately kept
The manual maintenance rules
clean_export_regions/export_all_regionsare kept. Unlike the two above, they're a documented in-file procedure (see the header comment inexport_for_nextstrain.smk) for re-curatinglat_longs.tsvandcolor_ordering.tsvafter an AWS data download, viascripts/check_missing_locations.py— operating on still-active files. If you'd rather these go too, say so and I'll drop them.Verification
clusterconfig acrossworkflow/,defaults/,docs/,nextstrain_profiles/.snakemake --profile nextstrain_profiles/nextstrain-ci -nis unchanged (37-job DAG, no errors) — confirming these rules weren't in any build's DAG.Test plan
🤖 Generated with Claude Code