Preprocess Subworkflow¶

Subworkflows combine tools in the right order to facilitate file targeting withing elvers. The "preprocess" subworkflow conducts read quality trimming. At the moment, this workflow consists of:

get_data - an elvers utility
trimmomatic
fastqc, run on both pre-trim and post-trim data

Quickstart¶

To run the preprocess subworkflow, run:

elvers examples/nema.yaml preprocess

Configuring the preprocess workflow¶

To set up your sample info and build a configfile, see Understanding and Configuring Workflows.

If you want to add the preprocess program parameters to a previously built configfile, run:

elvers config.yaml preprocess --print_params

A small set of parameters should print to your console:

  ####################  preprocess  ####################
get_data:
  download_data: false
  use_ftp: false
trimmomatic:
  adapter_file:
    pe_path: ep_utils/TruSeq3-PE-2.fa
    se_path: ep_utils/TruSeq3-SE.fa
  trim_cmd: ILLUMINACLIP:{}:2:40:15 LEADING:2 TRAILING:2 SLIDINGWINDOW:4:15 MINLEN:25
  extra: ''
fastqc:
  extra: ''

Override default params for any program by placing these lines in your yaml config file, and modifying values as desired. For more details, see Understanding and Configuring Workflows.For more on what parameters are available, see the docs for each specific program or utility rule: