v0.7.1

0.7.1 (2024-06-12)

Bug Fixes

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

v0.7.0

0.7.0 (2023-10-11)

Features

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

0.5.0 - 14/02/2023

Added

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

0.4.1

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

0.4.0 - 14/12/2022

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 - 26/10/2022

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 - 20/10/2022

Fixed

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

0.3.0 - 18/10/2022

Added

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

Changed

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

0.2.0 - 12/10/2022

Added

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

Changed

• Update mykrobe to v0.12 (WHO catalogue)

0.1.1 - 05/10/2022

0.1.1

Fixed

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