NF-CORE Cutandrun on Astrocyte

NF-CORE Cutandrun on Astrocyte

Introduction

nf-core/cutandrun is a best-practice bioinformatic analysis pipeline for CUT&RUN and CUT&Tag experimental protocols that were developed to study protein-DNA interactions and epigenomic profiling.

CUT&RUN

> Meers, M. P., Bryson, T. D., Henikoff, J. G., & Henikoff, S. (2019). Improved CUT&RUN chromatin profiling tools. eLife, 8. https://doi.org/10.7554/eLife.46314

CUT&Tag

> Kaya-Okur, H. S., Wu, S. J., Codomo, C. A., Pledger, E. S., Bryson, T. D., Henikoff, J. G., Ahmad, K., & Henikoff, S. (2019). CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nature Communications, 10(1), 1930. https://doi.org/10.1038/s41467-019-09982-5

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a portable, reproducible manner. It is capable of using containerisation and package management making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process, which makes it easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from https://github.com/nf-core/modules.

The pipeline has been developed with continuous integration (CI) and test driven development (TDD) at its core. nf-core code and module linting as well as a battery of over 100 unit and integration tests run on pull request to the main repository and on release of the pipeline. On official release, automated CI tests run the pipeline on a full-sized dataset on 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 be viewed on the nf-core website: https://nf-co.re/cutandrun/results.

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