v1.3

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

v1.2.2 - [16/03/23]

• Fix check_samplesheet.py bug

v1.2.1

v1.2.1 - [22/11/22]

• Fix Kraken 2 database bugs

v1.2

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

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

First release version of avantonder/bovisanalyzer.