Protein Assembly Subworkflow¶

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

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

Quickstart¶

To run the plass_assemble subworkflow, run:

elvers examples/nema.yaml plass_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 plass_assemble program parameters to a previously built configfile, run:

elvers config.yaml plass_assemble --print_params

A small set of parameters should print to your console:

 ####################  plass_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
plass:
  input_kmer_trimmed: true
  input_trimmomatic_trimmed: false
  add_single_to_paired: false # would you like to add the orphaned reads to the plass assembly?
  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: