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CHANGELOG.md

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XAVIER development version

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)

XAVIER 3.0.3

  • Bug fixes:
    • 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)
    • Reduce memory allocation. (#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 other CCBR pipelines. (#65, #67, @kelly-sovacool; #73, @kopardev)

XAVIER 3.0.2

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

XAVIER 3.0.1

Hotfixes for all!

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

XAVIER 3.0.0

  • added FRCE support.
  • adding $triggeroptions to snakemake cli.
  • using SLURM_SUBMIT_HOST as a secondary environmental variable to extract cluster name information on compute nodes.
  • func set_tmp() added to repeat tmpdir assignments across multiple rules.
  • vcf2maf fix applied.