xavier - XAVIER 3.2.1

• Added separate variable for control-freec genome fasta file (#169, @samarth8392)
• Updated default hg38 targets bed file to Agilent SureSelect v8 (#169, @samarth8392)
• Created a new hg38 config file (hg38_noalt) to use hg38 no alternate contigs reference genome (GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta). (#169, @samarth8392)
• Updated documentation to reflect the new genome config file (#169, @samarth8392)

- Python
Published by github-actions[bot] 9 months ago

xavier - XAVIER 3.2.0

• XAVIER now depends on ccbr_tools v0.4 for updated jobby & spooker utilities. (#165, @kelly-sovacool)

- Python
Published by github-actions[bot] 10 months ago

xavier - XAVIER 3.1.5

• Added cleanup script that deletes extra files from xavier pipeline output only on success (#154, @samarth8392)
• Fixed sequenza issue about not enough variants to solve model by removing the chrom-list filter (#154, @samarth8392)
• Added dryrun output to xavier output folder (#154, @samarth8392)
• Increased walltime for rule trimmomatic (#154, @samarth8392)
• Minor documentation updates. (#147, #149, @kelly-sovacool)
• Fix sample names in pairs file. (#151, @samarth8392)
• Updated base docker image for sequenza (#140, #154, @dnousome, @samarth8392)

- Python
Published by github-actions[bot] 10 months ago

xavier - v3.1.4

XAVIER 3.1.4

• Fix pySimpleGUI being removed from pip issue (#133, @samarth8392)
• Minor documentation improvements to README.md and GUI docs (@samarth8392)

- Python
Published by samarth8392 12 months ago

xavier - v3.1.3

XAVIER 3.1.3

• Fix breaking bug in varscan somaticFilter (#131, @dnousome)

- Python
Published by samarth8392 12 months ago

xavier - 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)

- Python
Published by github-actions[bot] over 1 year ago

xavier - 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)

- Python
Published by github-actions[bot] over 1 year ago

xavier - 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: https://github.com/CCBR/XAVIER/compare/v3.0.3...v3.1.0

- Python
Published by kelly-sovacool over 1 year ago

xavier - 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: https://github.com/CCBR/XAVIER/compare/v3.0.2...v3.0.3

- Python
Published by dnousome over 1 year ago

xavier - 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)

- Python
Published by kelly-sovacool about 2 years ago

xavier - v3.0.2

Documentation Updates Fixes for IUPAC codes

- Python
Published by dnousome about 2 years ago

xavier - 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

- Python
Published by dnousome over 2 years ago

xavier - v3.0

Increment version with GUI

- Python
Published by dnousome over 2 years ago