PBAssembleWithHifiasm

PBAssembleWithHifiasm

description
A workflow that performs single sample genome assembly on PacBio HiFi reads from one or more SMRT cells. The multiple SMRT cells data are merged prior to assembly.

Inputs

Required

  • ccs_fqs (Array[File], required): GCS path to CCS fastq 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

Optional

  • ref_fasta_for_eval (File?): Reference Fasta used for evaluating
  • CompressAndFinalizeMergedFQ.runtime_attr_override (RuntimeAttr?)
  • FinalizeHifiasmAlternateFA.name (String?)
  • FinalizeHifiasmAlternateFA.runtime_attr_override (RuntimeAttr?)
  • FinalizeHifiasmAlternateGFA.name (String?)
  • FinalizeHifiasmAlternateGFA.runtime_attr_override (RuntimeAttr?)
  • FinalizeHifiasmHapFAs.runtime_attr_override (RuntimeAttr?)
  • FinalizeHifiasmHapGFAs.runtime_attr_override (RuntimeAttr?)
  • FinalizeHifiasmPrimaryFA.name (String?)
  • FinalizeHifiasmPrimaryFA.runtime_attr_override (RuntimeAttr?)
  • FinalizeHifiasmPrimaryGFA.name (String?)
  • FinalizeHifiasmPrimaryGFA.runtime_attr_override (RuntimeAttr?)
  • FinalizeMergedFQ.keyfile (File?)
  • FinalizeMergedFQ.runtime_attr_override (RuntimeAttr?)
  • FinalizeQuastIndividualSummary.keyfile (File?)
  • FinalizeQuastIndividualSummary.name (String?)
  • FinalizeQuastIndividualSummary.runtime_attr_override (RuntimeAttr?)
  • FinalizeQuastReportHtml.keyfile (File?)
  • FinalizeQuastReportHtml.name (String?)
  • FinalizeQuastReportHtml.runtime_attr_override (RuntimeAttr?)
  • FinalizeQuastReports.runtime_attr_override (RuntimeAttr?)
  • FinalizeQuastSummaryAll.keyfile (File?)
  • FinalizeQuastSummaryAll.name (String?)
  • FinalizeQuastSummaryAll.runtime_attr_override (RuntimeAttr?)
  • MergeAllFastqs.runtime_attr_override (RuntimeAttr?)
  • primary_h0_h1_quast.runtime_attr_override (RuntimeAttr?)
  • Hifiasm.AssembleForAltContigs.runtime_attr_override (RuntimeAttr?)
  • Hifiasm.AssembleForHaplotigs.runtime_attr_override (RuntimeAttr?)

Defaults

  • Hifiasm.zones (String, default="us-central1-a us-central1-b us-central1-c us-central1-f")
  • MergeAllFastqs.prefix (String, default="merged"): prefix for output files

Outputs

  • merged_fq (File)
  • hifiasm_primary_gfa (File)
  • hifiasm_primary_tigs (File)
  • hifiasm_haploGFAs (File)
  • hifiasm_haplotigs (File)
  • hifiasm_alternate_gfa (File)
  • hifiasm_alternate_tigs (File)
  • quast_report_html (File?)
  • quast_report_in_various_formats (File?)
  • quast_summary_on_all (File?)
  • quast_summary_on_primary (File?)
  • quast_summary_on_H0 (File?)
  • quast_summary_on_H1 (File?)

Dot Diagram

PBAssembleWithHifiasm