RENEE: Rna sEquencing aNalysis pipElinE

RENEE 2.7.7

• Improve reliability and UX for reruns and student-partition usage: (#288, #289, #291, @kopardev)
  • Fix permissions when initializing output directories by normalizing copied resource permissions to be owner-writable/traversable (equivalent behavior to chmod -R u+wX on copied resources), preventing PermissionError when updating copied config files such as config/cluster.json.
  • Add partition-aware cluster limit enforcement for known partitions (currently Biowulf student), capping per-rule walltime/CPU requests in cluster.json to avoid scheduler rejections.
  • Add --max-jobs for renee run to control Snakemake SLURM fan-out; defaults to 10 for --partition student and 100 otherwise, with explicit user override taking priority.
  • Remove hardcoded Snakemake -j 500 from the runner path and propagate dynamic max-jobs through CLI → run orchestration → wrapper submission.
  • Improve terminal messaging with clearer phase banners, resolved run-parameter summary, labeled submission command/log paths, and post-submission monitoring hints.
  • Fix Python 3.12 regex escape warnings in setup.py by converting regex literals to raw strings.