RENEE 2.6.4

• Fix spelling of shared SIF directory on biowulf -- it is /data/CCBR_Pipeliner/SIFs with a lowercase "s" at the end. (#182, @kelly-sovacool)
• Raise an error if too few reads are left after trimming with cutadapt. (#184, @kelly-sovacool)
• Reformat GTF files during renee build that are missing 'gene_biotype' or 'gene_type' attributes in exons. (#185, @kelly-sovacool)
• Add support for the marmoset genome (mCalJac1 2021). (#185, @kelly-sovacool)

RENEE 2.6.3

• Upgrade containers to fix $PYTHONPATH clashes in fc_lane, inner_distance, tin, tin_merge, and rnaseq_multiqc. (#176, @kelly-sovacool)
• Fix error that prevented existing output directories from being re-run. (#176, @kelly-sovacool)
• Fix error in renee build where image_cache() wasn't imported. (#178, @kelly-sovacool)

RENEE 2.6.2

• Consolidate build_cluster.json into cluster.json. (#167, @kelly-sovacool)
• Remove unused miniconda container. (#168, @kelly-sovacool)
• Fix error in RSEQC rules. (#172, @kelly-sovacool)

RENEE 2.6.1

• New contributing guide available on GitHub and the documentation website. (#159, @kelly-sovacool)
• New renee debug subcommand to determine the base directory for debugging purposes. (#159, @kelly-sovacool)
• Fix renee cache subcommand to correctly read the container images config file. (#163, @kelly-sovacool)

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 to hg38_36 by default.
• 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 the ccbrpipeliner module.

Bug fixes

• Ensure renee build creates necessary config 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.
• 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)