### `Added` - [#576](https://github.com/nf-core/taxprofiler/pull/576) Sort input to krakenuniq to enable retrieval of cached batch tasks (❤️ to @muniheart for reporting and fix) - [#569](https://github.com/nf-core/taxprofiler/pull/569) Updated to nf-core pipeline template v3.1.2 (added by @sofstam) - [#571](https://github.com/nf-core/taxprofiler/pull/571) Updated to nf-core pipeline template v3.2.0 (added by @sofstam) - ### `Fixed` - [#580](https://github.com/nf-core/taxprofiler/pull/580) Minor documentation typo fixes (❤️ to @AlexHoratio for reporting and fix) - [#573](https://github.com/nf-core/taxprofiler/pull/573) Improved help messages and documentation to state many of the taxpasta related params require taxonomy files to be input (❤️ to @alexhbnr for reporting, fix by @jfy133) - [#578](https://github.com/nf-core/taxprofiler/pull/578) Fixed incorrect keyword in nextflow_schema.json (fix by @mashehu) - [#585](https://github.com/nf-core/taxprofiler/pull/585) Fixed code blocks (fix by @masheshu) - [#586](https://github.com/nf-core/taxprofiler/pull/586) Fixed wrong argument name for saving analysis reads (fix by @epstein6)

### `Added` - [#558](https://github.com/nf-core/taxprofiler/pull/558) Updated to nf-core pipeline template v3.1.0 (added by @LilyAnderssonLee) - [#565](https://github.com/nf-core/taxprofiler/pull/565) Updated to nf-core pipeline template v3.1.1 (added by @LilyAnderssonLee) ### `Fixed` - [#561](https://github.com/nf-core/taxprofiler/pull/561) Updated Centrifuge to fix internal error when running with conda (❤️ to @AnotherSimon for reporting, fix by @jfy133)

### `Added` - [#545](https://github.com/nf-core/taxprofiler/pull/545) Updated to nf-core pipeline template v3.0.2 (added by @LilyAnderssonLee & @jfy133) ### `Fixed` - [#550](https://github.com/nf-core/taxprofiler/pull/550/) Fixed a bug where single-end data with the same sample names that include `.` in it would overwrite output files (❤️ to @SannaAb for reporting, fixed by @Midnighter) - [#552](https://github.com/nf-core/taxprofiler/pull/552) Fixed the issue where nonpareil fails due to insufficient data for calculation caused by a missing PNG (❤️ to @Joon-Klaps for reporting, fixed by @LilyAnderssonLee) ### `Dependencies` ### `Deprecated`

### `Added` - [#417](https://github.com/nf-core/taxprofiler/pull/417) Added reference-free metagenome complexity/coverage estimation with Nonpareil (added by @jfy133) - [#466](https://github.com/nf-core/taxprofiler/pull/466) Input database sheets can specify a `db_type` column to distinguish between short- and long-read databases (added by @LilyAnderssonLee) - [#505](https://github.com/nf-core/taxprofiler/pull/505) Add small files to the file `tower.yml` (added by @LilyAnderssonLee) - [#508](https://github.com/nf-core/taxprofiler/pull/508) Add `nanoq` as a filtering tool for nanopore reads (added by @LilyAnderssonLee) - [#511](https://github.com/nf-core/taxprofiler/pull/511) Add `porechop_abi` as an alternative adapter removal tool for long reads nanopore data (added by @LilyAnderssonLee) - [#512](https://github.com/nf-core/taxprofiler/pull/512) Update all tools to the latest version and include nf-test (updated by @LilyAnderssonLee & @jfy133) - [#537](https://github.com/nf-core/taxprofiler/pull/537) Update the module `motus/merge` to the latest version (Updated by @sofstam & @LilyAnderssonLee) ### `Fixed` - [#518](https://github.com/nf-core/taxprofiler/pull/518) Fixed a bug where Oxford Nanopore FASTA input files would not be processed (❤️ to @ikarls for reporting, fixed by @jfy133) - [#523](https://github.com/nf-core/taxprofiler/pull/523) Removed hardcoded `-m lca` from GANON_CLASSIFY due to more options in new version of ganon (fixed by @LilyAnderssonLee & @jfy133) - [#531](https://github.com/nf-core/taxprofiler/pull/531) Fix FASTA input validation in schema allowing FASTQ extension, expand allowed FASTA extensions (fixed by @jfy133) - [#512](https://github.com/nf-core/taxprofiler/pull/532) Minor formatting and ordering improvements in MultiQC report (by @jfy133) - [#532](https://github.com/nf-core/taxprofiler/pull/532) - Added missing documentation behind the 'ignore' BRACKEN_BRACKEN error strategy (❤️ to @Mavti for reporting, fixed by @jfy133) - [#536](https://github.com/nf-core/taxprofiler/pull/536) - Redefine `contents_re` for filtlong to fix its missing from the MultiQC report (fixed by @LilyAnderssonLee) ### `Dependencies` | Tool | Previous version | New version | | --------- | ---------------- | ----------- | | bbmap | 39.01 | 39.06 | | bowtie2 | 2.4.4 | 2.5.2 | | bracken | 2.7 | 2.9 | | diamond | 2.0.15 | 2.1.8 | | ganon | 1.5.1 | 2.0.0 | | kraken2 | 2.1.2 | 2.1.3 | | krona | 2.8 | 2.8.1 | | megan | 6.24.20 | 6.25.9 | | metaphlan | 4.0.6 | 4.1.1 | | minimap2 | 2.24 | 2.28 | | motus | 3.0.3 | 3.1.0 | | multiqc | 1.21 | 1.25 | | samtools | 1.17 | 1.20 | ### `Deprecated`

### `Added` - [#487](https://github.com/nf-core/taxprofiler/pull/487) Updated to nf-core pipeline template v2.14.1 (added by @jfy133) ### `Fixed` - [#484](https://github.com/nf-core/taxprofiler/pull/484) Improved input validation to immediately fail if run accession IDs within a given sample ID are not unique (❤️ to @sofstam for reporting, fixed by @jfy133) - [#491](https://github.com/nf-core/taxprofiler/pull/491) Added flag to publish intermediate bracken files (❤️ to @ewissel for reporting, fixed by @sofstam and @jfy133) - [#489](https://github.com/nf-core/taxprofiler/pull/489) Fix KrakenUniq classified reads output format mismatch (❤️ to @SannaAb for reporting, fixed by @jfy133) - [#495](https://github.com/nf-core/taxprofiler/pull/495) Stop TAXPASTA failures when profiles do not have exact compositionality (fixes by @Midnighter, @jfy133) ### `Dependencies` | Tool | Previous version | New version | | -------- | ---------------- | ----------- | | KMCP | 0.9.1 | 0.9.4 | | TAXPASTA | 0.6.1 | 0.7.0 | ### `Deprecated` - [#492](https://github.com/nf-core/taxprofiler/pull/492) Removed `--kmcp_mode` parameter from KMCP to allow per database specification by setting in db_params in database sheet (fixed by @jfy133)

### `Added` - [#477](https://github.com/nf-core/taxprofiler/pull/477) Provide more emphasis and links to tutorials on how to retrieve and supply reference databases (❤️ to @vmkalbskopf for reporting, added by @jfy133) ### `Fixed` - [#476](https://github.com/nf-core/taxprofiler/pull/476/) Fixed bug in validating Bracken/Kraken/KMCP split database parameters (fixed by @LilyAnderssonLee) ### `Dependencies` ### `Deprecated`

### `Added` - [#454](https://github.com/nf-core/taxprofiler/pull/454) Updated to nf-core pipeline template v2.13.1 (added by @LilyAnderssonLee & @sofstam) - [#461](https://github.com/nf-core/taxprofiler/pull/461) Turned on 'strict' Nextflow evaluation runs (added by @jfy133) - [#461](https://github.com/nf-core/taxprofiler/pull/461) Optimised database compression so each compressed input database is untarred once, and shared amongst each run with different parameters (added by @jfy133) - [#461](https://github.com/nf-core/taxprofiler/pull/461) Added new parameter to optionally save uncompressed databases (added by @jfy133) - [#471](https://github.com/nf-core/taxprofiler/pull/471) Removed `-stub` run in the `download_pipeline.yml` because the pipeline does not support stub runs on dev (fixed by @LilyAnderssonLee) ### `Fixed` - [#336](https://github.com/nf-core/taxprofiler/issues/336) Replaced samplesheet check with nf-validation for both sample and database input sheets (fix by @LilyAnderssonLee) - [#460](https://github.com/nf-core/taxprofiler/issues/460) Corrected the channel transformations to combine Kaiju and mOTUs reports with their reference databases (fix by @Midnighter)

### `Added` - [#439](https://github.com/nf-core/taxprofiler/pull/439) Read deduplication with fastp (added by @maxibor) - [#440](https://github.com/nf-core/taxprofiler/pull/440) Include mention of pre-built kaiju databases in tutorial.md (added by @Joon-Klaps) - [#442](https://github.com/nf-core/taxprofiler/pull/442) Updated to nf-core pipeline template v2.12 (added by @sofstam) ### `Fixed` - [#444](https://github.com/nf-core/taxprofiler/pull/444) Centrifuge now uses dedicated tmp directory to hopefully prevent mkfifo clashes (❤️ to @erinyoung for reporting, fix by @jfy133) ### `Dependencies` | Tool | Previous version | New version | | ---------- | ---------------- | ----------- | | Centrifuge | 1.0.4_beta | 1.0.4.1 |