RENEE 2.7.6

Bug Fixes

• Python 3.12 Compatibility: Fixed ModuleNotFoundError: No module named 'rpds.rpds' when running on Python 3.12 (#282)
  • Upgraded ccbr_tools to v0.5.3 which includes a lazy-import fix for cffconvert to prevent loading the rpds C extension until the citation feature is actually needed
  • This allows RENEE to run on Python 3.12 without import errors

Related Issues & PRs

• Closes #282
• PR #283: Upgrade ccbr_tools to v0.5.3
• Upstream: CCBR/Tools#182

For installation and usage instructions, visit: https://ccbr.github.io/RENEE/

• Added more memory to rule validator. (#263, @samarth8392)
• New --time option for renee run and renee build to override the default SLURM walltime. (#269, @kelly-sovacool)
  • Also fix bug where --partition was not being propagated to the sbatch call.
• Documentation improvements: fix the jobby output filename and formatting problems. (#274, @kelly-sovacool)

• New --partition option for renee run and renee build to specify the SLURM partition. (#252, @kelly-sovacool)
  • This feature is necessary for users who do not have access to the norm partition on biowulf, such as students.
• Fix bug in phred_encoding.py that incorrectly detected Phred+33 files as Phred+64, causing BBMerge to fail. (#257, @kelly-sovacool)

• Bug fixes: (#246, @kelly-sovacool)
  • Increase memory for fastq screen.
  • Do not proceed to trimming if fastq validator fails.
  • Fix typo in docs.

• Fix typos in documentation. (#240, @ramlah7)
• Fix bug in renee build that caused dry run & run to fail with a syntax error. (#244, @kelly-sovacool)

• Improvements for fastq validator: (#224, @kelly-sovacool)
  • Increase default memory.
  • Capture stdout in a log file so the output is not deleted on failure.
• Fix broken symlinks for genome reference files on biowulf. (#226, @kelly-sovacool)

• Fix broken symlinks for genome reference files on biowulf. (#226, @kelly-sovacool)

• RENEE now depends on ccbr_tools v0.4 for updated jobby & spooker utilities. (#207, @kelly-sovacool)
• Add mmul10_108 (rhesus macaque) to list of reference genomes. (#212, @kelly-sovacool)
• Added support for new reference genomes on biowulf:
  • mm39_M36 (#199, @kelly-sovacool)
  • mm39_M37 (#220, @kelly-sovacool)
  • hg38_48 (#220, @kelly-sovacool)
• Fix --sif-cache example in docs. (#208, @kelly-sovacool)

• Minor CLI fixes. (#202, #203, @kelly-sovacool)

• Minor documentation updates. (#198, @kelly-sovacool)