From a11955603d515c9787d3f0e98a66ac643adae275 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Mon, 30 Jan 2023 10:50:31 +0100 Subject: [PATCH] Run CAT on bins and unbins --- CHANGELOG.md | 3 ++- workflows/mag.nf | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4bd1f573..d8b6f7c1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#353](https://github.com/nf-core/mag/pull/353) - Added the busco_clean parameter to optionally clean each BUSCO directory after a successful (by @prototaxites) - [#361](https://github.com/nf-core/mag/pull/361) - Added the skip_clipping parameter to skip read preprocessing with fastp or adapterremoval. Running the pipeline with skip_clipping, keep_phix and without specifying a host genome or fasta file skips the FASTQC_TRIMMED process (by @prototaxites) -- [#365](https://github.com/nf-core/mag/pull/365) - Adds CONCOCT as an additional (optional) binning tool (by @jfy133) +- [#365](https://github.com/nf-core/mag/pull/365) - Added CONCOCT as an additional (optional) binning tool (by @jfy133) - [#366](https://github.com/nf-core/mag/pull/366) - Added CAT_SUMMARISE process and cat_official_taxonomy parameter (by @prototaxites) - [#380](https://github.com/nf-core/mag/pull/380) - Added support for saving processed reads (clipped, host removed etc.) to results directory (by @jfy133) @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#340](https://github.com/nf-core/mag/pull/340),[#368](https://github.com/nf-core/mag/pull/368),[#373](https://github.com/nf-core/mag/pull/373) - Update to nf-core 2.7.2 `TEMPLATE` (by @jfy133, @d4straub, @skrakau) - [#373](https://github.com/nf-core/mag/pull/373) - Removed parameter `--enable_conda`. Updated local modules to new conda syntax and updated nf-core modules (by @skrakau) - [#350](https://github.com/nf-core/mag/pull/350) - Adds support for CheckM as alternative bin completeness and QC tool (added by @jfy133 and @skrakau) +- [#385](https://github.com/nf-core/mag/pull/385) - CAT also now runs on unbinned contigs as well as binned contigs (added by @jfy133) ### `Fixed` diff --git a/workflows/mag.nf b/workflows/mag.nf index c1eceda6..c52c5dd5 100644 --- a/workflows/mag.nf +++ b/workflows/mag.nf @@ -668,7 +668,7 @@ workflow MAG { ch_cat_db = CAT_DB_GENERATE.out.db } CAT ( - ch_input_for_postbinning_bins, + ch_input_for_postbinning_bins_unbins, ch_cat_db ) CAT_SUMMARY(