The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
-
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
-
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
- flag parsing is generic now.
- updated to latest version in https://github.com/DKFZ-ODCF/IndelCallingWorkflow/tree/hg38
-
conf/modules.config platypus arguments is fixed (now it is same as dkfz)
- FREQ based filtering is removed from bin/confidenceAnnotation_Indels.py.
Initial release of nf-core/platypusindelcalling, created with the nf-core template.
-
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.
-
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)
- FREQ-based filtering is removed from bin/confidenceAnnotation_Indels.py.
- nf-prov plugin added
- versioning of the pipeline is fixed