referenceGenomes.md

Reference Genomes Configuration

The pipeline needs a reference genome for alignment and annotation. All annotation data and paths must be defined/modified in the conf/genomes.conf files.

These paths can be supplied on the command line at run time (see the usage docs), 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.

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 must be specified in the config file genomes.conf.

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'
    }
    'OTHER-GENOME' {
      // [..]
    }
  }
  // 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.