Add workflow figure

.github/markdownlint.yml

@@ -3,3 +3,7 @@ default: true,
 line-length: false
 no-duplicate-header:
     siblings_only: true
+no-inline-html:
+    allowed_elements:
+        - img
+        - p

CHANGELOG.md

@@ -7,12 +7,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#124](https://github.com/nf-core/mag/pull/124) - Add worfklow overview figure to `README`
+
 ### `Changed`
 
 - [#123](https://github.com/nf-core/mag/pull/123) - Update to new nf-core 1.11 `TEMPLATE`
 
 ### `Fixed`
 
+- [#124](https://github.com/nf-core/mag/pull/124) - Fix description of `CAT` process in `output.md`
+
 ## v1.1.0 - 2020/10/06
 
 ### `Added`

README.md

@@ -14,7 +14,10 @@
 ## Introduction
 
 This pipeline is for assembly, binning, and annotation of metagenomes.
-It supports both short and long reads, quality trims the reads and adapters with [fastp](https://github.com/OpenGene/fastp) and [porechop](https://github.com/rrwick/Porechop), and performs basic QC with [fastqc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
+
+<p align="center">
+    <img src="docs/images/mag_workflow.png" alt="nf-core/mag workflow overview" width="60%">
+</p>
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
 
@@ -44,11 +47,13 @@ See [usage docs](https://nf-co.re/mag/usage) for all of the available options wh
 
 The nf-core/mag pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/mag/usage) and [output](https://nf-co.re/mag/output).
 
-The pipeline:
+In short, it supports both short and long reads, quality trims the reads and adapters with [fastp](https://github.com/OpenGene/fastp) and [porechop](https://github.com/rrwick/Porechop), and performs basic QC with [fastqc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
+The pipeline then:
 
 * assigns taxonomy to reads using [centrifuge](https://ccb.jhu.edu/software/centrifuge/) and/or [kraken2](https://github.com/DerrickWood/kraken2/wiki)
 * performs assembly using [megahit](https://github.com/voutcn/megahit) and [spades](http://cab.spbu.ru/software/spades/), and checks their quality using [quast](http://quast.sourceforge.net/quast)
 * performs metagenome binning using [metabat2](https://bitbucket.org/berkeleylab/metabat/src/master/), and checks the quality of the genome bins using [busco](https://busco.ezlab.org/)
+* assigns taxonomy to bins using [CAT](https://github.com/dutilh/CAT)
 
 Furthermore, the pipeline creates various reports in the results directory specified, including a [multiqc](https://multiqc.info/) report summarizing some of the findings and software versions.