{"repo":"nf-core/raredisease","free":true,"listed":false,"github":"https://github.com/nf-core/raredisease","clone":"git clone https://github.com/nf-core/raredisease.git","description":"Call and score variants from WGS/WES of rare disease patients.","language":"Nextflow","stars":122,"topics":["nf-core","nextflow","workflow","pipeline","wgs","wes","variant-calling","snv","structural-variants","variant-annotation"],"license":"MIT","category":"workflow-automation","readme_excerpt":"TOC - Introduction - Pipeline summary - Usage - Pipeline output - Credits - Contributions and Support - Citations Introduction nf-core/raredisease is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by MIP. [!NOTE] Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can ","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/raredisease/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}