Trimmomatic
note
Read trimming tool for Illumina NGS data.
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:
use_filename_as_sample_name: true
Note: The old trimmomatic.s_name_filenames option is deprecated and will be removed in a future version.
File search patterns
trimmomatic:
contents_re: ^Trimmomatic