Many nf-core pipelines need a reference genome for alignment, annotation or similar purposes.

Paths to such files can be supplied on the command line at run time, but for convenience it's often better to save these paths in a nextflow config file. See below for instructions on how to do this. Read Adding your own cluster configuration to find out how to set up custom config files.

Adding paths to a config file

Specifying long paths every time you run the pipeline is a pain. To make this easier, the pipeline comes configured to understand reference genome keywords which correspond to preconfigured paths, meaning that you can just specify --genome ID when running the pipeline.

Note that this genome key can also be specified in a config file if you always use the same genome.

To use this system, add paths to your config file using the following template:

params {
  genomes {
    'YOUR-ID' {
      fasta  = '<PATH TO FASTA FILE>/genome.fa'
      // [..]
  // Optional - default genome. Ignored if --genome 'OTHER-GENOME' specified on command line
  genome = 'YOUR-ID'

You can add as many genomes as you like as long as they have unique IDs.

Illumina iGenomes

To make the use of reference genomes easier, Illumina has developed a centralised resource called iGenomes. Multiple reference index types are held together with consistent structure for multiple genomes.

We have put a copy of iGenomes up onto AWS S3 hosting and this pipeline is configured to use this by default. The hosting fees for AWS iGenomes are currently kindly funded by a grant from Amazon. The pipeline will automatically download the required reference files when you run the pipeline. For more information about the AWS iGenomes, see iGenomes.

Downloading the files takes time and bandwidth, so we recommend making a local copy of the iGenomes resource. Once downloaded, you can customise the variable params.igenomes_base in your custom configuration file to point to the reference location. For example:

params.igenomes_base = '/path/to/data/igenomes/'


In any case if you need help with this, please don't hesitate to ask in our Slack channel for help in the #igenomes or #help channels.