From 5d6c1529ab727c93354ffac3865ab5a77efbe695 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Wed, 20 Dec 2023 10:13:31 +0100
Subject: [PATCH] Update README

---
 README.md | 34 +++++++++++++++++++++++++++-------
 1 file changed, 27 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index b2b55d9..c81f9ab 100644
--- a/README.md
+++ b/README.md
@@ -1,15 +1,17 @@
 # mtDNA-Server 2
+
 [![mtdna-server-2](https://github.com/genepi/mtdna-server-2/actions/workflows/run-tests.yml/badge.svg)](https://github.com/genepi/mtdna-server-2/actions/workflows/run-tests.yml)
 [![nf-test](https://img.shields.io/badge/tested_with-nf--test-337ab7.svg)](https://github.com/askimed/nf-test)
 
-Welcome to mtdna-Server 2. This repository includes the mtDNA-Server-2 Workflow ported to Nextflow. 
+Welcome to mtdna-Server 2. This repository includes the mtDNA-Server-2 Workflow ported to Nextflow.
 
 ## Access
-mtDNA-Server 2 is hosted as a service on our [mitoverse](https://mitoverse.i-med.ac.at/) platform.
 
+mtDNA-Server 2 is hosted as a service on our [mitoverse](https://mitoverse.i-med.ac.at/) platform.
 
 ## Documentation
-Documentation can be accessed [here](https://mitoverse.readthedocs.io). 
+
+Documentation can be accessed [here](https://mitoverse.readthedocs.io/mtdna-server/mtdna-server/).
 
 ## Local Installation
 
@@ -17,15 +19,25 @@ Documentation can be accessed [here](https://mitoverse.readthedocs.io).
 
 #### Requirements
 
+- Docker or Singularity
+- Java 14
 - Nextflow:
+
 ```
 curl -s https://get.nextflow.io | bash
 ```
 
-#### Execution
+#### Installation
+
+Build Docker image:
 
 ```
 docker build -t genepi/mtdna-server-2 . # don't ingore the dot here
+```
+
+#### Execution
+
+```
 nextflow run main.nf -c tests/test_single_bam.config -profile development
 ```
 
@@ -40,18 +52,26 @@ nextflow run main.nf -c tests/test_single_bam.config -profile development
 #### Installation
 
 - Install cloudgene3: `curl -s install.cloudgene.io | bash -s 3.0.0-beta4`
-- Download latest source code zip file from releases
 - Install mtDNA-Server 2 workflow: `./cloudgene install https://github.com/genepi/mtdna-server-2/archive/refs/tags/v2.0.0-beta2.zip`
 - Start cloudgene server: `./cloudgene server`
 - Open [http://localhost:8082](http://localhost:8082)
 - Login with default admin account: username `admin` and password `admin1978`
-- mtDNA-Server-2 can be tested with the following [test file](https://github.com/genepi/mtdna-server-2/raw/main/tests/data/bam/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam))
+- mtDNA-Server-2 can be tested with the following [test file](https://github.com/genepi/mtdna-server-2/raw/main/tests/data/bam/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam)
 
 ## Publication
+
 Weissensteiner H*, Forer L*, Fuchsberger C, Schöpf B, Kloss-Brandstätter A, Specht G, Kronenberg F, Schönherr S: mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud. Nucleic Acids Res. 44:W64-9, 2016. PMID: [27084948](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987870/)
 
 ## Contact
-Institute of Genetic Epidemiology, Medical University of Innsbruck 
+
+This software was developed at the [Institute of Genetic Epidemiology](https://genepi.i-med.ac.at/), [Medical University of Innsbruck](https://i-med.ac.at/)
+
+![](https://avatars2.githubusercontent.com/u/1942824?s=30) [Sebastian Schoenherr](mailto:sebastian.schoenherr@i-med.ac.at) ([@seppinho](https://twitter.com/seppinho))
+
+![](https://avatars2.githubusercontent.com/u/1931865?s=30) [Hansi Weissensteiner](mailto:hansi.weissensteiner@i-med.ac.at) ([@whansi](https://twitter.com/whansi))
+
+![](https://avatars2.githubusercontent.com/u/210220?s=30) [Lukas Forer](mailto:lukas.forer@i-med.ac.at) ([@lukfor](https://twitter.com/lukfor))
 
 ## License
+
 MIT Licensed.