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@kubranarci kubranarci released this 28 May 14:31
· 9 commits to main since this release

v2.0.0 - 28.05.2024

Added

  • assets/config/convertToStdVCF.json and bin/convertToStdVCF.py

    • Option to output VCF files (all) in standard format (4.2) is added. Also, TSV formatted confidence annotated/filtrated files are being converted into standard VCF.
  • MAFCommon tag is added to the INFO column to mark the common/recurrent artefacts.

  • Minor changes:

    • output names of the VCF files.

Fixed

  • Contig processing is only available for hg38 reference. ALT and/or HLA contigs can be given external in a file.

    • Automatic generation of HLA/ALT contigs is now possible through tumor BAM instead of fasta.
  • Conda links in nf-core modules are fixed.

    • NOTE: Conda environments are not available for the pipeline. Holding conda environment.yml links the same in default creates an error even when enable_conda is false.
  • bin/confidenceAnnotation_Indels.py

  • conf/modules.config platypus arguments are fixed (now it is the same as DKFZ/ODCF)

Dependencies

Deprecated

  • FREQ-based filtering is removed from bin/confidenceAnnotation_Indels.py.