The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- Fix Kraken 2 database bugs
- Add test profile and dataset so pipeline can be run with test.conf
- Rewrite python scripts
- Add skip_alignment, skip_kraken2 and skip_clusters parameters
- Update nextflow_schema.json
- Add parameters.md to docs
- Fix masking bug
- Output Picard MARKDUPLICATES metrics for multiQC
- Delete unnecessary subworkflows and modules
- Correct samtools index version from 1.14 to 1.15.1
- Edit documentation
- Standardise old modules to current syntax
- Add skip_alignment option to make alignment creation optional
- Edit modules.config to output low_quality_pseudogenomes.tsv
- Update spoligotype database
First release version of avantonder/bovisanalyzer.
Initial release of avantonder/bovisanalyzer, created with the nf-core template.