taxprofiler/CHANGELOG.md

# nf-core/taxprofiler: Changelog

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).

## dev

### `Added`

- [#276](https://github.com/nf-core/taxprofiler/pull/276) Implemented batching in the KrakenUniq samples processing. (added by @Midnighter)
- [#272](https://github.com/nf-core/taxprofiler/pull/272) - Add saving of final 'analysis-ready-reads' to dedicated directory. (❤️ to @alexhbnr for reporting, added by @jfy133)

### `Fixed`

- [#271](https://github.com/nf-core/taxprofiler/pull/271/files) Improved standardised table generation documentation nd mOTUs manual database download tutorial (♥ to @prototaxites for reporting, fix by @jfy133)
- [#269](https://github.com/nf-core/taxprofiler/pull/269/files) Reduced output files in AWS full test output due to very large files
- [#270](https://github.com/nf-core/taxprofiler/pull/270/files) Fixed warning for host removal index parameter, and improved index checks (♥ to @prototaxites for reporting, fix by @jfy133)
- [#274](https://github.com/nf-core/taxprofiler/pull/274/files) Substituted the samtools/bam2fq module with samtools/fastq module (fix by @sofstam)
- [#275](https://github.com/nf-core/taxprofiler/pull/275/files) Replaced function used for error reporting to more Nextflow friendly method (fix by @jfy133)
- [#286](https://github.com/nf-core/taxprofiler/pull/286/files) Runtime optimisation of MultiQC step via improved log file processing (fix by @Midnighter & @jfy133)

### `Dependencies`

### `Deprecated`

## v1.0.0 - Dodgy Dachshund [2023-03-13]

Initial release of nf-core/taxprofiler, created with the [nf-core](https://nf-co.re/) template.

- Add read quality control (sequencing QC, adapter removal and merging)
- Add read complexity filtering
- Add host-reads removal step
- Add run merging
- Add taxonomic classification
- Add taxon table standardisation
- Add post-classification visualisation

### `Added`

### `Fixed`

### `Dependencies`

### `Deprecated`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00			`# nf-core/taxprofiler: Changelog`

			`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).`

Update changelog after release 2023-03-13 11:21:37 +00:00			`## dev`

			### `Added`

Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> 2023-04-22 19:18:58 +00:00			`- [#276](https://github.com/nf-core/taxprofiler/pull/276) Implemented batching in the KrakenUniq samples processing. (added by @Midnighter)`
Add final documentation 2023-04-15 10:48:52 +00:00			`- [#272](https://github.com/nf-core/taxprofiler/pull/272) - Add saving of final 'analysis-ready-reads' to dedicated directory. (❤️ to @alexhbnr for reporting, added by @jfy133)`

Update changelog after release 2023-03-13 11:21:37 +00:00			### `Fixed`

Standardised taxon table and mOTU database docs improvement 2023-03-17 20:03:54 +00:00			`- [#271](https://github.com/nf-core/taxprofiler/pull/271/files) Improved standardised table generation documentation nd mOTUs manual database download tutorial (♥ to @prototaxites for reporting, fix by @jfy133)`
Fix broken check for host read removal index 2023-03-17 19:47:09 +00:00			`- [#269](https://github.com/nf-core/taxprofiler/pull/269/files) Reduced output files in AWS full test output due to very large files`
			`- [#270](https://github.com/nf-core/taxprofiler/pull/270/files) Fixed warning for host removal index parameter, and improved index checks (♥ to @prototaxites for reporting, fix by @jfy133)`
Update changelog 2023-03-23 14:34:47 +00:00			`- [#274](https://github.com/nf-core/taxprofiler/pull/274/files) Substituted the samtools/bam2fq module with samtools/fastq module (fix by @sofstam)`
update CHAGENLGO 2023-04-04 09:43:01 +00:00			`- [#275](https://github.com/nf-core/taxprofiler/pull/275/files) Replaced function used for error reporting to more Nextflow friendly method (fix by @jfy133)`
Update CHANGELOG 2023-04-20 14:01:22 +00:00			`- [#286](https://github.com/nf-core/taxprofiler/pull/286/files) Runtime optimisation of MultiQC step via improved log file processing (fix by @Midnighter & @jfy133)`
Standardised taxon table and mOTU database docs improvement 2023-03-17 20:03:54 +00:00
Update changelog after release 2023-03-13 11:21:37 +00:00			### `Dependencies`

			### `Deprecated`

Apply suggestions from code review 2023-03-13 09:57:36 +00:00			`## v1.0.0 - Dodgy Dachshund [2023-03-13]`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00
			`Initial release of nf-core/taxprofiler, created with the [nf-core](https://nf-co.re/) template.`

Update CHANGELOG for first release 2023-03-02 12:53:32 +00:00			`- Add read quality control (sequencing QC, adapter removal and merging)`
			`- Add read complexity filtering`
			`- Add host-reads removal step`
			`- Add run merging`
			`- Add taxonomic classification`
			`- Add taxon table standardisation`
			`- Add post-classification visualisation`

initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00			### `Added`

			### `Fixed`

			### `Dependencies`

			### `Deprecated`