millironx/taxprofiler
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Merge branch 'dev' into nf-core-template-merge-2.8

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James A. Fellows Yates 2023-05-02 13:17:18 +02:00 committed by GitHub
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CHANGELOG.md
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@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#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) - [#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)
- [#286](https://github.com/nf-core/taxprofiler/pull/286/files) Runtime optimisation of MultiQC step via improved log file processing (fix by @Midnighter & @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)
- [#289](https://github.com/nf-core/taxprofiler/pull/289/files) Pipeline updated to nf-core template 2.8 (fix by @Midnighter & @jfy133) - [#289](https://github.com/nf-core/taxprofiler/pull/289/files) Pipeline updated to nf-core template 2.8 (fix by @Midnighter & @jfy133)
- [#290](https://github.com/nf-core/taxprofiler/pull/286/files) Minor database input documentation improvements (♥ to @alneberg for reporting, fix by @jfy133)
### `Dependencies` ### `Dependencies`

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docs/usage.md
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@ -120,7 +120,7 @@ Column specifications are as follows:
nf-core/taxprofiler will automatically decompress and extract any compressed archives for you. nf-core/taxprofiler will automatically decompress and extract any compressed archives for you.
The (uncompressed) database paths (`db_path`) for each tool are expected to contain the contents of: The (uncompressed) database paths (`db_path`) for each tool are expected to contain:
- [**Bracken**:](#bracken-custom-database) output of the combined `kraken2-build` and `bracken-build` process. - [**Bracken**:](#bracken-custom-database) output of the combined `kraken2-build` and `bracken-build` process.
- [**Centrifuge**:](#centrifuge-custom-database) output of `centrifuge-build`. - [**Centrifuge**:](#centrifuge-custom-database) output of `centrifuge-build`.
@ -130,9 +130,9 @@ The (uncompressed) database paths (`db_path`) for each tool are expected to cont
- [**KrakenUniq**:](#krakenuniq-custom-database) output of `krakenuniq-build` command(s). - [**KrakenUniq**:](#krakenuniq-custom-database) output of `krakenuniq-build` command(s).
- [**MALT**](#malt-custom-database) output of `malt-build`. - [**MALT**](#malt-custom-database) output of `malt-build`.
- [**MetaPhlAn3**:](#metaphlan3-custom-database) output of with `metaphlan --install` or downloaded from links on the [MetaPhlAn3 wiki](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-3.0#customizing-the-database). - [**MetaPhlAn3**:](#metaphlan3-custom-database) output of with `metaphlan --install` or downloaded from links on the [MetaPhlAn3 wiki](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-3.0#customizing-the-database).
- [**mOTUs**:](#motus-custom-database) is composed of code and database together. - [**mOTUs**:](#motus-custom-database) the directory `db_mOTU/` that is downloaded via `motus downloadDB`.
Click the links in the list above for short quick-reference tutorials how to generate custom databases for each tool. > ℹ️ Click the links in the list above for short quick-reference tutorials how to generate custom databases for each tool.
## Running the pipeline ## Running the pipeline