Release v2.1.4

Changes

• Remove cleanup=true in config file

Release v2.1.3

Bugfixes

• The VAFator read filtering parameters were not passed at all when 0 was passed

Changes

• Default VAFator parameters for read filtering are now set to --mapping-quality 0 and --base-call-quality 0.

Release v2.1.2

Bugfixes:

• Update VAFator to version 1.1.4
  • Fixes TRON-Bioinformatics/vafator#19
  • Fixes TRON-Bioinformatics/vafator#18

Release v2.1.1

Fix

• The multiallelic filter was failing
• The option to skip the multiallelic filter was undocumented

Release v2.1.0

Changes

• Fix issue with VAFator integration
• Enable the support for any number of BAM files
• Add SnpEff for functional annotations

Release v2.0.0

Changes

• Migration of pipeline to Nextflow DSL 2
• CI environment migrated to GitHub actions
• Added several checks on the output VCFs during automated tests
• Integrate vafator as an optional step to annotate VCFs with allele frequencies in the same run
• Update bcftools to 1.14
• Conda dependencies are now managed at the module level avoiding conflicts between libraries

TronFlow variant normalization v1.1.1

Minor changes

• Cleans up intermediate files after correct execution

TronFlow variant normalization v1.1.0

Changes:

• Add support for VCFs without INFO/AD annotations using --vcf_without_ad
• Add better support for single VCFs through --input_vcf

TronFlow variant normalization v1.0.1

Changes:

• Fixes an issue with --help

TronFlow variant normalization v1.0.0

Changes:

• Integrate conda environments
• Makes more use of bcftools instead of vt due to better support.
• Automate tests
• Add clear examples to the README
• Add stats before and after normalization