Assemble Subworkflow¶

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

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

Quickstart¶

To run the assemble subworkflow, run:

elvers examples/nema.yaml assemble

Configuring the assemble subworkflow¶

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

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

elvers config.yaml assemble --print_params

A small set of parameters should print to your console:

 ####################  assemble  ####################
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
trinity:
  add_single_to_paired: false
  input_kmer_trimmed: true
  input_trimmomatic_trimmed: false
  max_memory: 30G
  seqtype: fq
  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: