Update README.md

README.md

@@ -7,6 +7,12 @@ mtDNA-Server 2 is a Nextflow DSL2 pipeline to accurately detect heteroplasmic an
 
 ![image](docs/images/report.png)
 
+### Documentation
+The documentation can be accessed [here](https://mitoverse.readthedocs.io/mtdna-server/mtdna-server/). 
+
+## Citation
+Weissensteiner H*, Forer L*, Kronenberg F, Schönherr S. [mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics](https://doi.org/10.1093/nar/gkae296). Nucleic Acids Res. 2024 May 6:gkae296. doi: 10.1093/nar/gkae296. Epub ahead of print. PMID: 38709886.
+
 ## Version History
 
 Release [v2.1.15](../../releases/tag/v2.1.15) - Add option for min mean coverage
@@ -21,76 +27,4 @@ Release [v2.1.11](../../releases/tag/v2.1.11) - Improve QC command, update to la
 
 Release [v2.1.10](../../releases/tag/v2.1.10) - Improved mutect2 support: create missing RG tags, write inidividual reference sequence on the fly, support complex ref tags.
 
-### Are your files not working?
-We want to steadily improve mtDNA-Server 2. If your files are not working, please feel free to create a [issue](https://github.com/genepi/mtdna-server-2/issues).
-
-## How to execute mtDNA-Server 2?
-mtDNA-Server 2 is available as a **hosted web-service** at the Medical University of Innsbruck or as a **Nextflow pipeline**.
-
-## Web Service
-
-mtDNA-Server 2 is hosted as a **free** service on our [mitoverse](https://mitoverse.i-med.ac.at/) platform.
-
-### Documentation
-
-The documentation can be accessed [here](https://mitoverse.readthedocs.io/mtdna-server/mtdna-server/). 
-
-## Nextflow Pipeline
-To run mtDNA-Server 2 via Nextflow, please execute the following steps. 
-
-### Quick Start
-
-1. Install [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation) (>=22.10.4)
-
-2. Run the pipeline on our test dataset and select either Docker, Singluarity or Slurm. 
-```
-nextflow run genepi/mtdna-server-2 -r v2.X.XX -profile test,<docker,singularity,slurm>
-```
-### Run Pipeline on own data
-To run mtDNA-Server 2 on your own data, create a [config file](tests/test_mitohpc_fusion.config) and run the following command:
-```
-nextflow run genepi/mtdna-server-2 -r v2.X.XX -c <your-config-file> -profile <docker,singularity,slurm>
-```
-
-### Parameters
-The following parameters can be set in the configuration file. 
-| Parameter            | Default Value        | Comment        |
-|----------------------|--------------|----------------|
-| project              | null         | Project name (required)   |
-| files                | null         | Input BAM files (required) |
-| mode                 | fusion       | Mode of operation (mutserve,mutect2,fusion) |
-| detection_limit      | 0.02         | Detection limit for heteroplasmic sites |
-| coverage_estimation  | on           | Coverage estimation enabled |
-| subsampling          | off          | Subsampling on/off |
-| subsampling_coverage | 2000         | Subsampling coverage |
-| mapQ                 | 20           | Mapping quality threshold |
-| baseQ                | 20           | Base quality threshold |
-| alignQ               | 30           | Alignment quality threshold |
-| min_mean_coverage               | 50           | Min Mean coverage |
-| output               | null         | Specific Output folder   |
-
-## Development
-```
-git clone https://github.com/genepi/mtdna-server-2
-cd mtdna-server-2
-docker build -t genepi/mtdna-server-2 . # don't ignore the dot
-nextflow run main.nf -profile test,development
-```
-
-## Publication
-Weissensteiner H*, Forer L*, Kronenberg F, Schönherr S. [mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics](https://doi.org/10.1093/nar/gkae296). Nucleic Acids Res. 2024 May 6:gkae296. doi: 10.1093/nar/gkae296. Epub ahead of print. PMID: 38709886.
-
-
-## Contact
-
-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:[email protected]) ([@seppinho](https://twitter.com/seppinho))
-
-![](https://avatars2.githubusercontent.com/u/1931865?s=30) [Hansi Weissensteiner](mailto:[email protected]) ([@whansi](https://twitter.com/whansi))
-
-![](https://avatars2.githubusercontent.com/u/210220?s=30) [Lukas Forer](mailto:[email protected]) ([@lukfor](https://twitter.com/lukfor))
-
-## License
 
-MIT Licensed.