Update README.md

README.md

@@ -1,15 +1,7 @@
-# ![nf-core/qcnorm](docs/images/nf-core-qcnorm_logo.png)
+# eQTL-Catalogue/qcnorm workflow
 
 **This pipeline will run QC measures of both genotype and phenotype data and will normalise quantified phenotypes**.
 
-[![Build Status](https://travis-ci.com/nf-core/qcnorm.svg?branch=master)](https://travis-ci.com/nf-core/qcnorm)
-[![GitHub Actions CI Status](https://github.com/nf-core/qcnorm/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/qcnorm/actions)
-[![GitHub Actions Linting Status](https://github.com/nf-core/qcnorm/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/qcnorm/actions)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)
-
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
-[![Docker](https://img.shields.io/docker/automated/nfcore/qcnorm.svg)](https://hub.docker.com/r/nfcore/qcnorm)
-
 ## Introduction
 
 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.
@@ -22,25 +14,19 @@ ii. Install one of [`docker`](https://docs.docker.com/engine/installation/), [`s
 
 iii. Download the pipeline and test it on a minimal dataset with a single command
 
-```bash
-nextflow run nf-core/qcnorm -profile test,<docker/singularity/conda/institute>
-```
 
 > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile institute` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
 
 iv. Start running your own analysis!
 
 <!-- TODO nf-core: Update the default command above used to run the pipeline -->
 
-```bash
-nextflow run nf-core/qcnorm -profile <docker/singularity/conda/institute> --reads '*_R{1,2}.fastq.gz' --genome GRCh37
-```
 
 See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
 
 ## Documentation
 
-The nf-core/qcnorm pipeline comes with documentation about the pipeline, found in the `docs/` directory:
+The eQTL-Catalogue/qcnorm pipeline comes with documentation about the pipeline, found in the `docs/` directory:
 
 1. [Installation](https://nf-co.re/usage/installation)
 2. Pipeline configuration
@@ -55,19 +41,5 @@ The nf-core/qcnorm pipeline comes with documentation about the pipeline, found i
 
 ## Credits
 
-nf-core/qcnorm was originally written by Nurlan Kerimov.
-
-## Contributions and Support
-
-If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
-
-For further information or help, don't hesitate to get in touch on [Slack](https://nfcore.slack.com/channels/qcnorm) (you can join with [this invite](https://nf-co.re/join/slack)).
-
-## Citation
-
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi. -->
-<!-- If you use nf-core/qcnorm for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
-
-You can cite the `nf-core` pre-print as follows: 
+eQTL-Catalogue/qcnorm was originally written by Nurlan Kerimov.
 
-> Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).