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Improve mOTUS database input desciption

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James Fellows Yates 2023-04-29 18:14:30 +02:00
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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