Nf-core is a community effort to collect a curated set of analysis pipelines, all of which are built using Nextflow. You will learn more about Nextflow in the next section, but knowing Nextflow is not a strict requirement to run nf-core pipelines.
To run an nf-core pipeline, you typically need to:
The main place to look for nf-core documentation is of course the nf-core website. There you will find plenty of training materials, and not all might be relevant for you (some are specific for users, and some for developers).
The best place to start are probably the Docs and Events sections. The first contains documentation on how to use nf-core pipelines and nf-core tools, and the latter contains details of past and future trainings around nf-core (talks, workshops, hackatons...).
Below we have selected a few of these materials to get you started.
The nf-core and nextflow tutorials below, explain how to install and run piplines from scratch, and we encourage you to follow these tutorials and try to install and run the pipelines by yourself. However, please note that at the BLIC, we have created modules for many of these pipelines (saving you from having to download the pipelines, creating config files specific for Myriad, etc). We will explain in more detail how to use the nf-core pipeline modules already available in Myriad in a later section.
Go to the Docs section and read all the Usage documentation, from "Getting Started" to "Troubleshooting". Then take the "Introduction to running nf-core pipelines" usage tutorial. Finally, if you are interested in nf-core as a developer, then take a look at the "Developer tutorials"
Another good short nf-core tutorial is the "nf-core" section of the "Introduction to Nextflow" tutorial developed by Sateesh Peri.
Another valuable resource for getting acquainted with nf-core pipelines is the weekly series of nf-core ByteSize Talks. These informative sessions are accessible on YouTube and cover a wide range of nf-core related material, including overviews of many of the nf-core pipelines like rnaseq, sarek, chipseq, and many more.
