XAVIER 3.1.2

• Fix minor bug in assess_significance.R script associated with rule freec_exome_somatic. (#120, @samarth8392)
• Fix bug in multiqc docker container, which caused an error when running xavier from ccbrpipeliner/7. (#123, @kelly-sovacool)
• Fix cache subcommand to correctly read the container images config file. (#124, @kelly-sovacool)

XAVIER 3.1.1

• New contributing guide available on GitHub and the documentation website. (#114, @kelly-sovacool)
• New xavier debug subcommand to determine the base directory for debugging purposes. (#114, @kelly-sovacool)
• Upgraded ccbr_wes_base docker to v1.1.0 with updated GATK version to v4.6.0.0 (#116, @samarth8392)
• Upgrade multiqc container to use v1.15. (#117, @kelly-sovacool)
• Upgrade memory for rule "bwa_mem" to 100G (#118, @samarth8392)

XAVIER 3.1.0

new features

• Add xavier gui subcommand to launch the graphical user interface. (#99, @kelly-sovacool)
  • Previously, xavier_gui (with an underscore) was a command in the ccbrpipeliner module.
• Provide default exome targets for hg38 and mm10, which can be overridden by the optional --targets argument. (#102, @kelly-sovacool)
  • Previously, the --targets argument was required with no defaults.
• Add new human test dataset (#27, @samarth8392)

bug fixes

• Fix bug in the GUI that always used the Agilent targets file by default, instead of picking based on the genome. (#108, @samarth8392)
• Fix bug in the driver script that caused the snakemake module not to be loaded on biowulf in some cases. (#111, @kelly-sovacool)
• Increased memory for rules: BWA mem, qualimap, kraken. gatk_contamination is no longer a localrule. (#89, @samarth8392)

documentation updates

• You can now cite XAVIER with the DOI 10.5281/zenodo.12727315. (#88, @kelly-sovacool)
• The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#150, @kelly-sovacool)
• Other minor documentation improvements. (#92, @kelly-sovacool; #93, @samarth8392)

Full Changelog: v3.0.3...v3.1.0

v3.0.3

What's Changed

• Use --rerun--incomplete Snakemake argument and fix bed. (#66, @dnousome)
• Fix final somatic merge (#70, @dnousome)
• Fix Varscan/Mutect2 output to keep Tumor Normal ordering. (#84, @dnousome)
• Fix issue #85 (#86, @samarth8392)
• Provide a more helpful error message when xavier is called with no arguments. (#75, @kelly-sovacool)
• Documentation improvements: (#78, @kelly-sovacool)
  • Document the release process for developers. (#63, @kelly-sovacool)
  • Create CITATION.cff to describe how to cite XAVIER. (#68, @kelly-sovacool)
• Sync GitHub Actions with with other CCBR pipelines. (#65, #67, @kelly-sovacool; #73, @kopardev)

Full Changelog: v3.0.2...v3.0.3

v3.0.2

• Documentation updates for GUI and other genome references
• Additional IUPAC changes to play nice with GATK tools (non ACGTN codes convert to N)

v3.0.1

Hotfixes for all!

• Increased memory for somatic merge rule
• Fixed spooker/runner calls for run info
• Fixed vcf2maf which missed the Intersection of calls

v3.0

Increment version with GUI