referenceGenomes.md

Configuration of the reference genomes

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

These paths can be supplied on the command line at run time (see the usage documentation), but for convenience it's often better to save these paths in a Nextflow config file. See below the 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 conf/genomes.conf.

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

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

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