Kmer_trim Subworkflow¶

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

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

Quickstart¶

To run the kmer_trim subworkflow, run:

elvers examples/nema.yaml kmer_trim

Configuring the kmer_trim subworkflow¶

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

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

elvers config.yaml kmer_trim --print_params

A small set of parameters should print to your console:

 ####################  kmer_trim  ####################
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
  extra: ''
  trim_cmd: ILLUMINACLIP:{}:2:40:15 LEADING:2 TRAILING:2 SLIDINGWINDOW:4:15 MINLEN:25
fastqc:
  extra: ''
khmer:
  C: 3
  Z: 18
  coverage: 20
  diginorm: true
  extra: ''
  ksize: 20
  memory: 4e9
  #######################################################

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: