RENEE 2.5.12

• Minor documentation improvements. (#100, @kelly-sovacool)
• Fix RNA report bug, caused by hard-coding of PC1-3, when only PC1-2 were generated. (#104, @slsevilla)
• Allow printing the version or help message even if singularity is not in the path. (#110, @kelly-sovacool)
• Fix RSeQC environments:
  • Set RSeQC envmodule version to 4.0.0, which synchronizes it with the version in the docker container used by singularity. (#122, @kelly-sovacool)
  • Update docker with RSeQC's tools properly added to the path. (#123, @kelly-sovacool)

RENEE 2.5.11

• Create a citation file to describe how to cite RENEE. (#86, @kelly-sovacool)
• Fix: set HPC-specific fastq screen config and kraken DB paths for Biowulf and FRCE. (#78, @kelly-sovacool)
  • Previously, FRCE users were required to set --shared-resources,
    which were kept in a location on FRCE not under version control.
    This change brings the paths under version control so they're easier to recover if deleted.
• Fix permissions to allow read/write access to the scripts dir which caused rNA report to fail (#91, @slsevilla)
• Fix RSEM reference and rRNA interval list paths in FRCE-specific config files (#85, @kelly-sovacool & @slsevilla)
• Fix bug which caused incorrect genome annotation JSON files to be used (#87, @kelly-sovacool)
• Set default temporary directory depending on HPC platform. (#98, @kelly-sovacool)

RENEE v2.5.10

Fix a bug that caused slurm jobs to fail (#74, @kopardev)

RENEE v2.5.9

• Fix bugs that prevented single-end data from running through the pipeline. (#58, @kelly-sovacool)
• Increase wall time for kraken and bbmerge rules. (#68, @slsevilla)