Canu

Canu

description
A workflow that runs the Canu 3-step assembly (correct, trim, assemble). Tested on a small genome (malaria ~23mb), larger genomes may require some changes including tweaks to the default resource allocation. Currently assumes nanopore reads

Inputs

Required

  • assemble_error_rate (Float, required): parameter to canu's 'correctedErrorRate'
  • correct_error_rate (Float, required): parameter to canu's 'correctedErrorRate'
  • genome_size (Int, required): estimate on genome size (parameter to canu's 'genomeSize')
  • prefix (String, required): prefix to output files
  • reads (File, required): reads to be canu-corrected
  • trim_error_rate (Float, required): parameter to canu's 'correctedErrorRate'

Optional

  • Assemble.runtime_attr_override (RuntimeAttr?)
  • Correct.runtime_attr_override (RuntimeAttr?)
  • Trim.runtime_attr_override (RuntimeAttr?)

Outputs

  • fa (File)

Dot Diagram

Canu