nf-core/references is a bioinformatics pipeline that build references.
This repo contains references yaml files that describe references.
These references yaml files 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_source/ folder will contain references yaml files that are source references yaml files used to generate/update references that will be stored in AWS iGenomes as currently described in the igenomes/ folder.
The igenomes/ folder contains references yaml files 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_yaml_asset.sh script.
The igenomes_no_base/ folder contains references yaml files that have the same information as described before, but without the igenomes_base params.
The genomes_source/ folder contains references yaml files that are source references yaml files, that will be used later on to generate/update genomes in AWS iGenomes.
The genomes/ folder contains references yaml files 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.
The genomes_no_base/ folder contains references yaml files that have the same information as described before, but without the igenomes_base params.
To use a references yaml file in an nf-core pipeline, a link toward the raw reference yaml file can be used.
Either using the main branch, or a specific commit for versioning and reproducibility purposes.
For further information or help, don't hesitate to get in touch on the Slack #references channel (you can join with this invite).