chore(deps): update dependency snakemake to v9.6.1

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
snakemake	9.5.1 -> 9.6.1

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Release Notes

snakemake/snakemake (snakemake)

v9.6.1

Compare Source

Bug Fixes

• fix bug in workflow.source_path causing non-cached source files when called from input functions (#​3638) (9980bfe)

v9.6.0

Compare Source

Features

• Prefer papermill to nbconvert (#​2857) (4263b03)

Bug Fixes

• DeprecationWarning when using snakemake.utils.validate (#​3420) (cf72427)
• display group jobs on dryrun (#​3435) (3bebef4)
• expandvars for special profile keys (#​3597) (4020188)
• fix bug causing --precommand to not being executed before each remote job (#​3625) (e59d125)
• improved toggle switch behavior in reports (#​3623) (0c4bd23)
• pass envvars defined via the envvars directive to remote jobs (#​3626) (d4890b4)
• remove wms arg, update logging cli docs (#​3622) (3a9a5ac)
• typo in CondaEnvDirSpec.eq (issue #​3192) (#​3613) (f4c107f)
• Unclear handling of params overriding with inheritance (#​3624) (077ac4a)

Documentation

• Added snakemake command to execute the rule plot_with_python (#​3608) (bd99c11)
• Updated Reporting Section of The Tutorial(Interaction, Visualization, and Reporting with Snakemake) (#​3606) (91e90ba)
• Updated Requirement Section of The Tutorial With Warning of Not Installing The Tools Manually (#​3607) (3bd114b)
• Updated Wrapper Version in Tutorial and Used Simple Rule For Consistency & Ease (#​3605) (b3bcc21)

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[github-actions]

🦙 MegaLinter status: ⚠️ WARNING

Descriptor	Linter	Files	Fixed	Errors	Warnings	Elapsed time
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⚠️ BASH	bash-exec	6		1	0	0.01s
✅ BASH	shellcheck	6		0	0	0.15s
✅ BASH	shfmt	6	0	0	0	0.59s
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✅ DOCKERFILE	hadolint	131		0	0	28.69s
✅ JSON	jsonlint	20		0	0	0.19s
✅ JSON	v8r	22		0	0	14.09s
⚠️ MARKDOWN	markdownlint	269	0	306	0	20.78s
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✅ PYTHON	ruff	222	0	0	0	0.81s
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✅ REPOSITORY	git_diff	yes		no	no	0.75s
⚠️ REPOSITORY	grype	yes		30	no	31.92s
✅ REPOSITORY	secretlint	yes		no	no	8.89s
✅ REPOSITORY	syft	yes		no	no	2.48s
✅ REPOSITORY	trivy	yes		no	no	12.04s
✅ REPOSITORY	trivy-sbom	yes		no	no	20.69s
✅ REPOSITORY	trufflehog	yes		no	no	4.45s
✅ SPELL	cspell	730		0	0	14.73s
✅ SPELL	lychee	351		0	0	25.11s
✅ XML	xmllint	3	0	0	0	1.26s
✅ YAML	prettier	160	0	0	0	4.17s
✅ YAML	v8r	103		0	0	19.38s
✅ YAML	yamllint	161		0	0	3.62s

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