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60 lines
2.9 KiB
Markdown
60 lines
2.9 KiB
Markdown
# nf-core/taxprofiler: Changelog
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## v1.1.0dev - [date]
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### `Added`
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- [#276](https://github.com/nf-core/taxprofiler/pull/276) Implemented batching in the KrakenUniq samples processing. (added by @Midnighter)
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- [#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)
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### `Fixed`
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- [#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)
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- [#269](https://github.com/nf-core/taxprofiler/pull/269/files) Reduced output files in AWS full test output due to very large files
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- [#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)
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- [#274](https://github.com/nf-core/taxprofiler/pull/274/files) Substituted the samtools/bam2fq module with samtools/fastq module (fix by @sofstam)
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- [#275](https://github.com/nf-core/taxprofiler/pull/275/files) Replaced function used for error reporting to more Nextflow friendly method (fix by @jfy133)
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- [#285](https://github.com/nf-core/taxprofiler/pull/285/files) Fixed overly large log files in Kraken2 output (♥ to @prototaxites for reporting, fix by @Midnighter & @jfy133)
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- [#286](https://github.com/nf-core/taxprofiler/pull/286/files) Runtime optimisation of MultiQC step via improved log file processing (fix by @Midnighter & @jfy133)
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- [#289](https://github.com/nf-core/taxprofiler/pull/289/files) Pipeline updated to nf-core template 2.8 (fix by @Midnighter & @jfy133)
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- [#290](https://github.com/nf-core/taxprofiler/pull/286/files) Minor database input documentation improvements (♥ to @alneberg for reporting, fix by @jfy133)
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### `Dependencies`
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| Tool | Previous version | New version |
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| ------- | ---------------- | ----------- |
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| MultiQC | 1.13 | 1.14 |
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### `Deprecated`
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## v1.0.1 - Dodgy Dachshund Patch [2023-05-15]
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### `Added`
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### `Fixed`
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- [#291](https://github.com/nf-core/taxprofiler/pull/291) - Fix Taxpasta not receiving taxonomy directory (❤️ to @SannaAb for reporting, fix by @jfy133)
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## v1.0.0 - Dodgy Dachshund [2023-03-13]
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Initial release of nf-core/taxprofiler, created with the [nf-core](https://nf-co.re/) template.
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- Add read quality control (sequencing QC, adapter removal and merging)
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- Add read complexity filtering
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- Add host-reads removal step
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- Add run merging
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- Add taxonomic classification
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- Add taxon table standardisation
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- Add post-classification visualisation
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### `Added`
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### `Fixed`
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### `Dependencies`
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### `Deprecated`
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