Changelog

All notable changes to this project will be documented in this file.

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

0.7.1 (2024-06-12)

Bug Fixes

update rasusa usage for latest version (#57) (1f3d32d)

0.7.0 (2023-10-11)

Features

expose parameter for subsampling [#53] (3d0411e)

unreleased

0.6.0

Added

Stats from mapping to the decontamination database are now added to the stats report

0.5.0

Added

Read stats (subsampled reads) from nanoq in tbpore process. The stats file will be in the output directory.

0.4.1

Changed

Removed 'subsampled' from the VCF path [#49]

0.4.0

Added

download subcommand to download and validate the decontamination database
sorting of the decontaminated fastq file to ensure subsampling is reproducible regardless of whether a combined fastq or directory of fastqs is provided [#48]

Changed

Default (expected) location of the decontamination database is now ${HOME}/.tbpore/decontamination_db/remove_contam.map-ont.mmi
Variant filtering params
- minimum depth changed from 0 to 5
- minimum variant quality (QUAL) score from 85 to 25
- minimum mapping quality from 0 to 30

Removed

Usage of deprecated iteritems function from pandas. This will remove an annoying deprecated warning when running tbpore cluster

0.3.2

Changed

When --name is not given, take name to be the filename minus the fastq (and optional gz) suffix. Previously, we took everything before the first . [#45]

0.3.1

Fixed

data/ and external_scripts/ directories were not having their contents included in site-packages when installing from sdist

0.3.0

Added

Ability to specify the path to the cache directory (--cache) [#43]

Changed

Default cache dir is now ${HOME}/.cache [#43]
Default output directory for all subcommands is now the current directory

0.2.0

Added

Ability to specify a different path for the decontamination database (--db) and metadata file (--metadata) [#34]

Changed

Update mykrobe to v0.12 (WHO catalogue)

0.1.1

Fixed

Added missing, required files and directories, .config.yaml, data/, external_scripts/, and CHANGELOG.md to distribution

0.1.0

Added

First release - so everything you see is new!