The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Full Changelog: https://github.com/ghga-de/nf-snvcalling/compare/v1.0...v2.0.0
Initial release of ghga-de/nf-snvcalling, 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.
-
MAFCommontag 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.
-
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
- FREQ-based filtering is removed from bin/confidenceAnnotation_SNVs.py.
- bcftools1.9 biocontainers docker changed with kubran/bcftools:v1.9
- 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
- nf-prov plugin is added.
- 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)
- upgrade samtools version for cram handling (modules/local/grep_samplename.nf)
- edit nextflow version to latest (nextflow.config)