Trimmomatic

The module parses the stderr output, that can be captured by directing it to a file e.g.:

trimmomatic command 2> trim_out.log

By default, the module generates the sample names based on the input FastQ file names in the command line used by Trimmomatic. If you prefer, you can tell the module to use the filenames as sample names instead. To do so, use the following config option:

trimmomatic:
  s_name_filenames: true

File search patterns

trimmomatic:
  contents: Trimmomatic