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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:
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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
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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.https://eresearchqut.atlassian.net/wiki/spaces/EG/pages/edit-v2/2261090311#epi2me
Examples of pipelines used at QUT:
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