2. Nextflow pipeline repositories
- Marie-Emilie Gauthier
nf-core
What is nf-core?
nf-core is a community-led project to develop a set of best-practice pipelines built using Nextflow workflow management system. Pipelines are governed by a set of guidelines, enforced by community code reviews and automatic code testing. The diagram below showcases the key aspects of nf-core and is divided into three sections:
the Deploy section includes features like Stable pipelines, Centralized configs, List and update pipelines, and Download for offline us.
the Participate section highlights Documentation, Slack workspace, Twitter updates, and Hackathons.
the Develop section emphasizes the Starter template, Code guidelines, CI code linting and tests, and Helper tools.
What are nf-core pipelines?
nf-core pipelines are an organised collection of Nextflow scripts, other non-nextflow scripts (written in any language), configuration files, software specifications, and documentation hosted on GitHub. There is generally a single pipeline for a given data and analysis type e.g. There is a single pipeline for bulk RNA-Seq. All nf-core pipelines are open source.
A defined pipeline structure is used to deploy new pipelines (https://nf-co.re/docs/contributing/pipelines/pipeline_file_structure) and bioinformatics tools are available as a list of modules and subworkflows.
Searching for available nf-core pipelines
Go to https://nf-co.re/pipelines
Narrow search by typing relevant term, for example ‘rna-seq’:
Pipelines can be sorted by Latest release, Name or Stars:
Examples of pipelines used at QUT:
nf-core support
For support with Nextflow, see https://nf-co.re/join.
For instance, there is a very active slack community for nf-core users (https://nfcore.slack.com/)
epi2me workflows
EPI2ME Labs maintains a collection of bioinformatics workflows tailored to Oxford Nanopore Technologies long-read sequencing data. They are curated and actively maintained by experts in long-read sequence analysis.
Examples of pipelines used at QUT: