Refactor for advanced workflows and update cluster basics

[juliendrapeau]

This pull request reorganizes and modernizes the HPC onboarding documentation, adding new beginner-friendly guides, improving SSH setup instructions, updating SLURM script templates, and introducing sections on containers and workflow automation. The changes aim to streamline the onboarding process, clarify best practices, and provide ready-to-use scripts and configs.

Resolves #2.

Major documentation improvements:

• Added a new 01-cluster-basics/README.md with a step-by-step beginner guide for connecting, transferring files, and submitting jobs on HPC clusters, including cluster overviews and links to official resources.
• Rewrote the main README.md to provide a high-level overview and clear navigation through the repository, pointing users to the new modular guides.
• Added new introductory guides for containers (02-docker-apptainer/README.md) and workflow automation with Snakemake (03-snakemake/README.md). [1] [2]

SSH setup and configuration:

• Introduced an SSH quick start guide (ssh/README.md) and a sample SSH config file (ssh/config) to simplify secure, passwordless access to clusters using aliases and key management. [1] [2]

SLURM job script updates:

• Updated SLURM script templates (base_script.sh, advanced_script.sh, advanced_script_gpus.sh) to reflect current cluster partition names, Python versions, and best practices for virtual environments and GPU usage. (Fafe8724R1, [1] [2] [3] [4]

Content reorganization and cleanup:

• Moved and renamed files for a clearer structure, grouping scripts and documentation by topic and removing redundant or outdated explanations (e.g., more_on_shell_scripts/README.md was removed in favor of the new guides). [1] [2] [3] [4] [5]

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References:
[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11]

[JeremieGince]

This is a great PR, minor changes required.

[juliendrapeau]

Agreed on all counts. PR #8 addresses these comments.