minor fixes

Fixed

• add cram/crai files to input list (assets/schema_input.json)
• add only a warn about the indices does not exists in converttovcf.json (bin/convertToStdVCF.py)
• change default arg for ENSEMBL VEP (conf/modules.config)
• set TMPDIR to working dir (modules/local/check_if_corrupted.nf)
• edit nextflow version to latest (nextflow.config)

v2.0.0 main 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

  • Flag parsing is generic now.
  • Updated to the latest version in https://github.com/DKFZ-ODCF/IndelCallingWorkflow/tree/hg38

• 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.

v1.1 beta

• Descriptions on how to use VEP annotation are improved
• Annotation file channels fixed

v1.0

initial release