update workflowimage

Author: Joon-Klaps

README.md

@@ -23,9 +23,7 @@
 
 ## Pipeline summary
 
-![viral-genie-workflow](images/metromap_style_pipeline_workflow_viralgenie.png)
-
-Tools given for each step can change as benchmarking is in progress.
+![viralgenie-workflow](docs/images/metromap_style_pipeline_workflow_viralgenie.png)
 
 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 2. Performs optional read pre-processing

docs/README.md

@@ -12,4 +12,21 @@ description: A metagenomics analysis pipeline for eukaryotic viruses written in
 
 ==}
 
---8<-- "README.md:6:"
+
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
+[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/Joon-Klaps/viralgenie)
+
+[![GitHub Actions CI Status](https://github.com/Joon-Klaps/viralgenie/actions/workflows/ci.yml/badge.svg)](https://github.com/Joon-Klaps/viralgenie/actions?query=workflow%3A%22nf-core+CI%22)
+[![GitHub Actions Linting Status](https://github.com/Joon-Klaps/viralgenie/actions/workflows/linting.yml/badge.svg)](https://github.com/Joon-Klaps/viralgenie/actions?query=workflow%3A%22nf-core+linting%22)
+
+<!-- [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23viralgenie-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/viralgenie)-->
+
+## Introduction
+
+**Joon-Klaps/viralgenie** is a bioinformatics best-practice analysis pipeline for reconstructing consensus genomes and to identify intra-host variants from metagenomic sequencing data or enriched based sequencing data like hybrid capture.
+
+## Pipeline summary
+
+![viralgenie-workflow](images/metromap_style_pipeline_workflow_viralgenie.png)
+
+--8<-- "README.md:27:"

docs/usage.md

@@ -1,7 +1,5 @@
 # Usage
 
-!!! warning "Please read this documentation on the [Viralgenie website](https://github.io/Joon-Klaps/viralgenie/usage)"
-
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows: