build(deps): Update snakemake requirement from <=7.32.4 to <=8.29.0

[dependabot]

Updates the requirements on snakemake to permit the latest version.

Release notes

Sourced from snakemake's releases.

v8.29.0

8.29.0 (2025-02-27)

Features

• provide mechanism to link between report items (snakemake.report_href, see docs) (#3224) (a024e60)
• toggles for binary labels in report (#3296) (7690998)

Bug Fixes

• add missing @​conda annotations (#3298) (0b541cc)
• properly handle remote storage when waiting for pipes (#3317) (9f7e092)
• provide proper error messages if output file preparation (pipe, mkdir) fails (#3309) (77ef176)
• record file extension (e.g. .tsv) in between workflow cache records in order to avoid that files of the wrong format are erroneously returned by the cache. This will lead to some cache misses. But avoiding errors induced by the previous behavior of ignoring file extensions when seeking for cache records is more important. (#3314) (4912f00)
• sort results lexicographically by labels in their order of appearance (#3293) (a19a0ac)

Documentation

• update best practices (7270eb3)

Changelog

Sourced from snakemake's changelog.

8.29.0 (2025-02-27)

Features

• provide mechanism to link between report items (snakemake.report_href, see docs) (#3224) (a024e60)
• toggles for binary labels in report (#3296) (7690998)

Bug Fixes

• add missing @​conda annotations (#3298) (0b541cc)
• properly handle remote storage when waiting for pipes (#3317) (9f7e092)
• provide proper error messages if output file preparation (pipe, mkdir) fails (#3309) (77ef176)
• record file extension (e.g. .tsv) in between workflow cache records in order to avoid that files of the wrong format are erroneously returned by the cache. This will lead to some cache misses. But avoiding errors induced by the previous behavior of ignoring file extensions when seeking for cache records is more important. (#3314) (4912f00)
• sort results lexicographically by labels in their order of appearance (#3293) (a19a0ac)

Documentation

• update best practices (7270eb3)

8.28.0 (2025-02-12)

Features

• do not fail if --cache is active but no SNAKEMAKE_OUTPUT_CACHE env var is defined. Instead, print a warning that explains the options. (#3270) (9610f7c)

Bug Fixes

• do not use outdated metadata for rerun triggers (only warn about it) (#3259) (d766a48)
• ensure that exceptions print storage queries instead of local copies of remote files (#3258) (e5d8ec1)
• fix error message of evaluate helper function (#3282) (9483a64)
• Revert cleaning of env vars in apptainer (#3285) (e79a51b)

Performance Improvements

• compare checksums of input files <= 1MB (before (10KB) (#3267) (ba017bb)
• query updated input files in parallel (#3266) (bc4fcee)

Documentation

• Adds instructions for using syntax highlighting with lazy.nvim (#3246) (7a75043)
• Fix typos in basic API example (#3277) (8782219)

8.27.1 (2025-01-08)

... (truncated)

Commits

• beb9915 chore(main): release 8.29.0 (#3294)
• 4912f00 fix: record file extension (e.g. .tsv) in between workflow cache records in o...
• 9f7e092 fix: properly handle remote storage when waiting for pipes (#3317)
• 77ef176 fix: provide proper error messages if output file preparation (pipe, mkdir) f...
• 04f89d3 fix
• 9a3e29f chore: fix if syntax
• 99ae9b2 dbg
• 7690998 feat: toggles for binary labels in report (#3296)
• 4818b80 chore: use locally deployed minio instead of play.min.io for storage testing ...
• 784e867 best practices for reporting
• Additional commits viewable in compare view

You can trigger a rebase of this PR by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)

Note
Automatic rebases have been disabled on this pull request as it has been open for over 30 days.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 68.96%. Comparing base (9d8d492) to head (7bb318a).
⚠️ Report is 4 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #307      +/-   ##
==========================================
- Coverage   69.40%   68.96%   -0.44%     
==========================================
  Files          37       37              
  Lines        3219     3219              
==========================================
- Hits         2234     2220      -14     
- Misses        985      999      +14     

see 1 file with indirect coverage changes

---

Continue to review full report in Codecov by Sentry.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 9d8d492...7bb318a. Read the comment docs.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.