Releases: mbhall88/tbpore
Releases · mbhall88/tbpore
v0.7.1
v0.7.0
0.5.0 - 14/02/2023
Added
- Read stats (subsampled reads) from
nanoq
intbpore process
. The stats file will be in the output directory.
0.4.1
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 runningtbpore 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/
andexternal_scripts/
directories were not having their contents included in site-packages when installing from sdist
0.3.0 - 18/10/2022
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/
, andCHANGELOG.md
to distribution