Merge pull request #49 from avantonder/apha

Apha

Author: avantonder

CHANGELOG.md

@@ -3,9 +3,23 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 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
+- Fix `Kraken 2` database bugs
 
 ## v1.2 - [14/11/22]
 

README.md

@@ -87,7 +87,6 @@ Alternatively the samplesheet.csv file created by [`nf-core/fetchngs`](https://n
         --input samplesheet.csv \
         --reference <REFERENCE FASTA> \
         --kraken2db minikraken2_v1_8GB \
-        --brackendb minikraken2_v1_8GB \
         --outdir <OUTDIR>
     ```
 

assets/spoligotype_db.tsv

@@ -2207,21 +2207,43 @@
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