{"repo":"nf-core/chipseq","free":true,"listed":false,"github":"https://github.com/nf-core/chipseq","clone":"git clone https://github.com/nf-core/chipseq.git","description":"ChIP-seq peak-calling, QC and differential analysis pipeline.","language":"Nextflow","stars":242,"topics":["nf-core","nextflow","workflow","chip-seq","chromatin-immunoprecipitation","peak-calling","chip","pipeline","macs2"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nfcore/chipseq is a bioinformatics analysis pipeline used for Chromatin ImmunoPrecipitation sequencing (ChIP-seq) data. On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. The dataset consists of FoxA1 (transcription factor) and EZH2 (histone,mark) IP experiments from Franco et al. 2015 (GEO: GSE59530, PMID: 25752574) and Popovic et al. 2014 (GEO: GSE57632, PMID: 25188243), respectively. 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 running the full-sized tests can be viewed on the nf-core website. 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! Online videos A short talk about the history, current status and functionality on offer in this pipeline was given","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/chipseq/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."}