From 44286bf96dde6e0246a69395f378d8ddbde4aaa8 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Sat, 29 Apr 2023 18:14:30 +0200 Subject: [PATCH 1/2] Improve mOTUS database input desciption --- docs/usage.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index a98da95..ed63e44 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -120,7 +120,7 @@ Column specifications are as follows: 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. - [**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). - [**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). -- [**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 From 2dc8a88b673ea678e6aa1f4e9aa4f33bfde69860 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Sat, 29 Apr 2023 18:17:09 +0200 Subject: [PATCH 2/2] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2e3d35e..bd5deb6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#275](https://github.com/nf-core/taxprofiler/pull/275/files) Replaced function used for error reporting to more Nextflow friendly method (fix by @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) +- [#290](https://github.com/nf-core/taxprofiler/pull/286/files) Minor database input documentation improvements (♥ to @alneberg for reporting, fix by @jfy133) ### `Dependencies`