ONTAssembleWithCanu

ONTAssembleWithCanu

description
A workflow that performs single sample genome assembly on ONT reads from one or more flow cells. The workflow merges multiple samples into a single BAM prior to genome assembly and variant calling.

Inputs

Required

  • gcs_fastq_dir (String, required): GCS path to unaligned CCS BAM files
  • gcs_out_root_dir (String, required): GCS bucket to store the reads, variants, and metrics files
  • participant_name (String, required): name of the participant from whom these samples were obtained
  • prefix (String, required): prefix for output files
  • ref_map_file (File, required): table indicating reference sequence and auxillary file locations

Optional

  • ComputeGenomeLength.runtime_attr_override (RuntimeAttr?)
  • FinalizeAsmPolished.keyfile (File?)
  • FinalizeAsmPolished.name (String?)
  • FinalizeAsmPolished.runtime_attr_override (RuntimeAttr?)
  • FinalizeAsmUnpolished.keyfile (File?)
  • FinalizeAsmUnpolished.name (String?)
  • FinalizeAsmUnpolished.runtime_attr_override (RuntimeAttr?)
  • FinalizeQuastReportHtml.keyfile (File?)
  • FinalizeQuastReportHtml.name (String?)
  • FinalizeQuastReportHtml.runtime_attr_override (RuntimeAttr?)
  • FinalizeQuastReportTxt.keyfile (File?)
  • FinalizeQuastReportTxt.name (String?)
  • FinalizeQuastReportTxt.runtime_attr_override (RuntimeAttr?)
  • ListFilesOfType.runtime_attr_override (RuntimeAttr?)
  • MedakaPolish.runtime_attr_override (RuntimeAttr?)
  • MergeFastqs.runtime_attr_override (RuntimeAttr?)
  • Quast.runtime_attr_override (RuntimeAttr?)
  • CallAssemblyVariants.AlignAsPAF.runtime_attr_override (RuntimeAttr?)
  • CallAssemblyVariants.Paftools.runtime_attr_override (RuntimeAttr?)
  • Canu.Assemble.runtime_attr_override (RuntimeAttr?)
  • Canu.Correct.runtime_attr_override (RuntimeAttr?)
  • Canu.Trim.runtime_attr_override (RuntimeAttr?)

Defaults

  • assemble_error_rate (Float, default=0.15): stringency for overlaps in Canu's assemble step
  • correct_error_rate (Float, default=0.15): stringency for overlaps in Canu's correction step
  • medaka_model (String, default="r941_prom_high_g360"): Medaka polishing model name
  • trim_error_rate (Float, default=0.15): stringency for overlaps in Canu's trim step
  • ListFilesOfType.recurse (Boolean, default=false)
  • MedakaPolish.zones (String, default="us-central1-a us-central1-b us-central1-c us-central1-f")
  • MergeFastqs.prefix (String, default="merged"): prefix for output files
  • Quast.is_large (Boolean, default=false)

Outputs

  • asm_unpolished (File)
  • asm_polished (File)
  • paf (File)
  • paftools_vcf (File)
  • quast_report_html (File)
  • quast_report_txt (File)
  • quast_summary (Map[String,String])

Dot Diagram

ONTAssembleWithCanu