build(deps-dev): update snakemake requirement from ^8.18.0 to ^9.0.1

[dependabot]

Updates the requirements on snakemake to permit the latest version.

Release notes

Sourced from snakemake's releases.

v9.0.1

9.0.1 (2025-03-14)

Bug Fixes

• group job error call (#3448) (3d53863)

Changelog

Sourced from snakemake's changelog.

9.0.1 (2025-03-14)

Bug Fixes

• group job error call (#3448) (3d53863)

9.0.0 (2025-03-14)

⚠ BREAKING CHANGES

• Logging refactor & add LoggerPluginInterface (#3107)

Features

• #3412 - keep shadow folder of failed job if --keep-incomplete flag is set. (#3430) (22978c3)
• add flag --report-after-run to automatically generate the report after a successful workflow run (#3428) (b0a7f03)
• add flatten function to IO utils (#3424) (67fa392)
• add helper functions to parse input files (#2918) (63e45a7)
• Add option to print redacted file names (#3089) (ba4d264)
• add support for validation of polars dataframe and lazyframe (#3262) (c7473a6)
• added support for rendering dag with mermaid js (#3409) (7bf8381)
• adding --replace-workflow-config to fully replace workflow configs (from config: directive) with --configfile, instead of merging them (#3381) (47504a0)
• Dynamic module name (#3401) (024dc32)
• Enable saving and reloading IOCache object (#3386) (c935953)
• files added in rule params with workflow.source_path will be available in used containers (#3385) (a6e45bf)
• Fix keep_local in storage directive and more freedom over remote retrieval behaviour (#3410) (67b4739)
• inherit parameters of use rule and extend/replace individual items them when using 'with' directive (#3365) (93e4b92)
• Logging refactor & add LoggerPluginInterface (#3107) (86f1d6e)
• Maximal file size for checksums (#3368) (b039f8a)
• Modernize package configuration using Pixi (#3369) (77992d8)
• multiext support for named input/output (#3372) (05e1378)
• optionally auto-group jobs via temp files in case of remote execution (#3378) (cc9bba2)

Bug Fixes

• --delete-all-output ignores --dry-run (#3265) (23fef82)
• 3342 faster touch runs and warning messages for non-existing files (#3398) (cd9c3c3)
• add default value to max-jobs-per-timespan (#3043) (2959abe)
• checkpoints inside modules are overwritten (#3359) (fba3ac7)
• Convert Path to IOFile (#3405) (c58684c)
• Do not perform storage object cleanup with --keep-storage-local-copies set (#3358) (9a6d14b)
• edgecases of source deployment in case of remote execution (#3396) (5da13be)
• enhance error message formatting for strict DAG-building mode (#3376) (a1c39ee)
• fix bug in checkpoint handling that led to exceptions in case checkpoint output was missing upon rerun (#3423) (8cf4a2f)
• force check all required outputs (#3341) (495a4e7)
• group job formatting (#3442) (f0b10a3)
• in remote jobs, upload storage in topological order such that modification dates are preserved (e.g. in case of group jobs) (#3377) (eace08f)

... (truncated)

Commits

• 2a16ae1 chore(main): release 9.0.1 (#3451)
• 3d53863 fix: group job error call (#3448)
• 466823b Docs/migration (#3446)
• 4d4d1a8 chore: fix xrootd test (#3450)
• 0a75d6c chore: dbg sh fail (#3447)
• 4d778fb chore(main): release 9.0.0 (#3380)
• f0b10a3 fix: group job formatting (#3442)
• a305d2c ci: switch to maintained version of release-please, add FPAT to enable CI run...
• ba4d264 feat: Add option to print redacted file names (#3089)
• fba3ac7 fix: checkpoints inside modules are overwritten (#3359)
• Additional commits viewable in compare view

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