Primer File

You can set the primer file and the the primer options in the config.yaml file. You’ll want to change the fields under trim_reads. To learn more about the options, see the help fields below, and see the documentation at http://www.usadellab.org/cms/?page=trimmomatic

trim_reads:
    primerfile:
        default:
        help:  'Primer File'
    primerseed:
        default: 2
        help:   'seed mismatches'
    palindromeclip:
        default: 30
        help: 'palindrome clip threshold'
    simpleclip:
        default: 20
        help: 'simple clip threshold'

The available options are:

primerfile: path to the primer file
primerseed: seed mismatches
palindromeclip: palindrome clip threshold
simpleclip: simple clip threshold