avantonder/bovisanalyzer: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.3 - [08/02/24]

Rename --subsampling_off to --skip_subsampling
Remove --brackendb parameter as redundant. Bracken will now use the database location specified with --krakendb.
Update spoligotype database file (January 2024)
Update TB-profiler to version 5.0.1 and remove external database as this version has Zwyer lineages incorporated
Remove SpoTyping and use spoligotyping results from TB-profiler instead
Change %Mapped column header in read_stats_summary.csv to %TrimMapped so as to make clearer that the % of reads mapped is based on the number of trimmed reads
Documentation updated

v1.2.2 - [16/03/23]

Fix check_samplesheet.py bug

v1.2.1 - [22/11/22]

Fix Kraken 2 database bugs

v1.2 - [14/11/22]

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

v1.1 - [26/10/22]

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

v1.0 - [21/10/22]

First release version of avantonder/bovisanalyzer.

v1.0dev - [28/04/22]

Initial release of avantonder/bovisanalyzer, created with the nf-core template.