v2.0.0 main release

v2.0.0 - 24.06.2024

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.

• modules/local/sort_nonstandard_vcf.nf

  • sorted output for nonstandard raw 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_SNVs.py

  • Flag parsing is generic now.

• Better dealing with ALT and HLA contigs.

  • modules/local/get_contigs.nf fixed.
  • ALT and HLA contig extraction is fixed
  • Turn off error when there is no alignment to contigs.

• bin/vcf_pileup_compare_allin1_basecount.pl

  • sorted results

• modules/local/seq_context_annotator.nf

  • sorted results

Dependencies

Deprecated

• FREQ-based filtering is removed from bin/confidenceAnnotation_SNVs.py.
• bcftools1.9 biocontainers docker changed with kubran/bcftools:v1.9

What's Changed

• 20 output proper vcf by @kubranarci in #33
• re-arrange resources for dkfz cluster by @kubranarci in #34
• 35 raw vcf is not sorted by @kubranarci in #36

Full Changelog: v1.0...v2.0.0