Merge pull request #644 from jfy133/new-images

[Merge #642 #641 first] New images with updated workflows

Author: jfy133

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 - [#640](https://github.com/nf-core/eager/issues/640) - Added a pre-metagenomic screening filtering of low-sequence complexity reads with `bbduk`
 - [#583](https://github.com/nf-core/eager/issues/583) - Added `mapDamage2` rescaling of BAM files to remove damage
+- Updated usage (merging files) and workflow images reflecting new functionality.
 
 ### `Fixed`
 

README.md

@@ -22,7 +22,7 @@
 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. The pipeline pre-processes raw data from FASTQ inputs, or preprocessed BAM inputs. It can align reads and performs extensive general NGS and aDNA specific quality-control on the results. It comes with docker, singularity or conda containers making installation trivial and results highly reproducible.
 
 <p align="center">
-    <img src="docs/images/output/overview/eager2_workflow.png" alt="nf-core/eager schematic workflow" width="70%"
+    <img src="docs/images/usage/eager2_workflow.png" alt="nf-core/eager schematic workflow" width="70%"
 </p>
 
 ## Quick Start
@@ -119,7 +119,7 @@ Additional functionality contained by the pipeline currently includes:
 A graphical overview of suggested routes through the pipeline depending on context can be seen below.
 
 <p align="center">
-    <img src="docs/images/output/overview/eager2_metromap_complex.png" alt="nf-core/eager metro map" width="70%"
+    <img src="docs/images/usage/eager2_metromap_complex.png" alt="nf-core/eager metro map" width="70%"
 </p>
 
 ## Documentation