From 66a0bfd59415620cedde9322fc13897a3e72d313 Mon Sep 17 00:00:00 2001 From: Kaur Alasoo Date: Mon, 21 Dec 2020 19:13:14 +0200 Subject: [PATCH] Update README.md --- README.md | 34 +++------------------------------- 1 file changed, 3 insertions(+), 31 deletions(-) diff --git a/README.md b/README.md index e5244f9..7325f4f 100644 --- a/README.md +++ b/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. @@ -22,9 +14,6 @@ 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, -``` > 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. @@ -32,15 +21,12 @@ iv. Start running your own analysis! -```bash -nextflow run nf-core/qcnorm -profile --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 - - - - -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).