Skip to content

Latest commit

 

History

History
91 lines (51 loc) · 2.79 KB

CHANGELOG.md

File metadata and controls

91 lines (51 loc) · 2.79 KB
Raw

nf-core/platypusindelcalling: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

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.

  • minor changes:

    • output names

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 is fixed.

    • NOTE: Conda enviroments are not available for the pipeline. Holding conda environment.yml links the same in default creates error even when enable_conda is false.

  • bin/confidenceAnnotation_Indels.py

  • conf/modules.config platypus arguments is fixed (now it is same as dkfz)

Dependencies

Deprecated

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

v1.0dev

Initial release of nf-core/platypusindelcalling, created with the nf-core template.

Added

Fixed

Dependencies

Deprecated

v2.0.0 - [09.10.2024]

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.

v2.0.1 - [09.10.2024]

Added

  • nf-prov plugin added

Fixed

  • versioning of the pipeline is fixed