nf-core/references is a bioinformatics pipeline that build references.

This repo contains datasheets yaml files that describe references.

These datasheets can either be used to build references using the nf-core/references pipeline, or to be used as a reference in an nf-core pipeline.

The igenomes/ folder contains datasheets that describe what is currently available in AWS iGenomes, plus any meta data. These files can be used to start a pipeline, when using the corresponding schema with an up to date pipeline. They are initially generated by the generate_datasheet.sh script.

The genomes_source/ folder contains datasheets that are source datasheets, that will be used later on to generate/update genomes in the references cloud storage.

The genomes/ folder contains datasheets that describe what is currently available s3://nf-core-references, plus any meta data. These files can be used to start a pipeline, when using the corresponding schema with an up to date pipeline.

To use a references yaml file in an nf-core pipeline, a link toward the raw reference yaml file can be used. Using the latest branch will ensure that the latest datasheets are used. It is recommended to use a specific commit to pin a specific version of a datasheet and the corresponding references.

For further information or help, don't hesitate to get in touch on the Slack #references channel (you can join with this invite).