Changes after review from @d4straub

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#366](https://github.com/nf-core/mag/pull/366) - Added CAT_SUMMARISE process and cat_official_taxonomy parameter (by @prototaxites)
 - [#372](https://github.com/nf-core/mag/pull/372) - Allow CAT_DB to take an extracted database as well as a tar.gz file.
 - [#380](https://github.com/nf-core/mag/pull/380) - Added support for saving processed reads (clipped, host removed etc.) to results directory (by @jfy133)
+- [#394](https://github.com/nf-core/mag/pull/380) - Added GUNC for additional chimeric bin/contamination QC (added by @jfy13)
 
 ### `Changed`
 

docs/output.md

@@ -416,7 +416,9 @@ For each bin or refined bin the median sequencing depth is computed based on the
 
 </details>
 
-### QC for metagenome assembled genomes with BUSCO
+### QC for metagenome assembled genomes
+
+#### BUSCO
 
 [BUSCO](https://busco.ezlab.org/) is a tool used to assess the completeness of a genome assembly. It is run on all the genome bins and high quality contigs obtained by the applied binning and/or binning refinement methods (depending on the `--postbinning_input` parameter). By default, BUSCO is run in automated lineage selection mode in which it first tries to select the domain and then a more specific lineage based on phylogenetic placement. If available, result files for both the selected domain lineage and the selected more specific lineage are placed in the output directory. If a lineage dataset is specified already with `--busco_reference`, only results for this specific lineage will be generated.
 
@@ -455,8 +457,6 @@ Besides the reference files or output files created by BUSCO, the following summ
 
 </details>
 
-### QC for metagenome assembled genomes
-
 #### CheckM
 
 [CheckM](https://ecogenomics.github.io/CheckM/) CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage