Upgrade to Snakemake version 9

[fgypas]

Description

Upgrade Snakemake version 9

Fixes #190

Type of change

Please delete options that are not relevant.

• [ ] Bug fix (non-breaking change which fixes an issue)
• [X] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
• [ ] Documentation updated

Conventional Commits guidelines

• [ ] I made sure the PR title follows the https://www.conventionalcommits.org/en/v1.0.0/

Changes to workflow inputs (sample table and/or configs)

• major (add BREAKING CHANGE: in the beginning of the PR title)
  • more fields/properties are required
  • existing ones are dropped entirely
• minor (add feat: in the beginning of the PR title)
  • optional fields/properties are added
  • required ones are made optional

Changes to workflow outputs

• major (add BREAKING CHANGE: in the beginning of the PR title)
  • changes lead to removal/change of existing outputs (format or location)
• minor (add feat: in the beginning of the PR title)
  • additional outputs are generated
  • content (but not format or location) of existing outputs changes

Everything else: patch (add any other conventional commit in the beginning of the PR title)

Checklist:

• [X] My code changes follow the style of this project
• [X] I have performed a self-review of my own code
• [X] I have commented my code, particularly in hard-to-understand areas
• [X] My changes generate no new warnings
• [ ] I have added tests that prove my fix is effective or that my feature works
• [X] New and existing tests pass locally with my changes
• [ ] I have updated the project's documentation

Summary by Sourcery

Upgrade Snakemake requirement to version 9.3.3 and standardize core dependencies on the conda-forge channel in both development and production environment files.

Enhancements:

• Bump Snakemake requirement to >=9.3.3 in environment.yml and environment.dev.yml
• Switch biopython, conda, graphviz, pyopenssl, python, and unzip dependencies to conda-forge channel in both environment files

[sourcery-ai[bot]]

Reviewer's Guide

The PR upgrades the Snakemake dependency to version 9.3.3 and standardizes all environment YAML dependencies to the conda-forge channel, including adding an explicit conda package in both development and production config files.

File-Level Changes

Change	Details	Files
Bump Snakemake to version >=9.3.3	Updated Snakemake constraint in environment.yml Updated Snakemake constraint in environment.dev.yml	install/environment.yml install/environment.dev.yml
Migrate dependencies to conda-forge channel	Prefixed biopython, graphviz, pyopenssl, python, and unzip with conda-forge Ensured consistent channel usage across both YAMLs	install/environment.yml install/environment.dev.yml
Add explicit conda package	Inserted conda-forge::conda entry into environment.yml Inserted conda-forge::conda entry into environment.dev.yml	install/environment.yml install/environment.dev.yml

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#190	Upgrade the Snakemake version to version 9 or higher.	✅
#190	Update the yaml files to reflect the Snakemake version upgrade.	✅

Possibly linked issues

• #190: The PR updates the Snakemake dependency in environment files to version 9.3.3, addressing the issue's request.

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[fgypas]

Hi @ninsch3000 Thank very much for looking into it. I made an update to use the general executor plugin and updated the corresponding profiles. Can you please give it a try in the cluster? Thank you in advance for your help.