Releases: CCBR/RENEE
Releases · CCBR/RENEE
RENEE 2.6.0
New features
- Support hg38 release 45 on biowulf & FRCE. (#127, @kelly-sovacool)
- hg38 genome index files now include decoy & virus sequences. (#136, @kelly-sovacool)
- Additionally,
--genome
is no longer required and is set tohg38_36
by default.
- Additionally,
- Set default shared singularity SIF directory for biowulf and frce. (#94, @kelly-sovacool)
- Add
renee gui
subcommand to launch the graphical user interface. (#94, @kelly-sovacool)- Previously,
renee_gui
(with an underscore) was a command in theccbrpipeliner
module.
- Previously,
Bug fixes
- Ensure
renee build
creates necessaryconfig
directory during initialization. (#139, @kelly-sovacool) - Run
rsem-generate-data-matrix
to create gene and isoform matrix files. (#149, @kelly-sovacool) - Fix bug in the driver script that caused the snakemake module not to be loaded on biowulf in some cases. (#154, @kelly-sovacool)
Documentation updates
- Minor documentation improvements. (#132, #135, #152, @kelly-sovacool)
- Add GUI instructions to the documentation website. (#38, @samarth8392)
- The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#150, @kelly-sovacool)
- Show the name of the pipeline rather than the python script for CLI help messages. (#131, @kelly-sovacool)
- Added Expected output tab to the documentation website and updated FAQs (#156, @samarth8392)
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.
- Previously, FRCE users were required to set
- 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
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)