PBCCSIsoSeq

PBCCSIsoSeq

description
A workflow that performs CCS correction and IsoSeq processing on PacBio HiFi reads from a single flow cell. The workflow shards the subreads into clusters and performs CCS in parallel on each cluster. Error-corrected reads are then processed with PacBio's IsoSeq software. A number of metrics and figures are produced along the way.

Inputs

Required

  • barcode_file (File, required): GCS path to the fasta file that specifies the expected set of multiplexing barcodes
  • ccs_bams (Array[File], required): GCS path to CCS BAM files
  • ccs_pbis (Array[File], required): GCS path to CCS BAM .pbi indices
  • gcs_out_root_dir (String, required): GCS bucket to store the corrected/uncorrected reads, variants, and metrics files
  • participant_name (String, required): name of the participant from whom these samples were obtained
  • ref_map_file (File, required): table indicating reference sequence and auxillary file locations

Optional

  • AlignTranscripts.library (String?)
  • BamToBed.runtime_attr_override (RuntimeAttr?)
  • ClusterTranscripts.runtime_attr_override (RuntimeAttr?)
  • CollapseTranscripts.runtime_attr_override (RuntimeAttr?)
  • Demultiplex.runtime_attr_override (RuntimeAttr?)
  • DetailedDemuxReportPNG.runtime_attr_override (RuntimeAttr?)
  • FinalizeAlignedBai.keyfile (File?)
  • FinalizeAlignedBai.runtime_attr_override (RuntimeAttr?)
  • FinalizeAlignedBam.keyfile (File?)
  • FinalizeAlignedBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeAlignedPbi.keyfile (File?)
  • FinalizeAlignedPbi.runtime_attr_override (RuntimeAttr?)
  • FinalizeAlignedTranscriptsBai.keyfile (File?)
  • FinalizeAlignedTranscriptsBai.name (String?)
  • FinalizeAlignedTranscriptsBai.runtime_attr_override (RuntimeAttr?)
  • FinalizeAlignedTranscriptsBam.keyfile (File?)
  • FinalizeAlignedTranscriptsBam.name (String?)
  • FinalizeAlignedTranscriptsBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeAlignedTranscriptsBed.keyfile (File?)
  • FinalizeAlignedTranscriptsBed.name (String?)
  • FinalizeAlignedTranscriptsBed.runtime_attr_override (RuntimeAttr?)
  • FinalizeBam.keyfile (File?)
  • FinalizeBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeCollapsedTranscripts.keyfile (File?)
  • FinalizeCollapsedTranscripts.name (String?)
  • FinalizeCollapsedTranscripts.runtime_attr_override (RuntimeAttr?)
  • FinalizeDemultiplexCounts.keyfile (File?)
  • FinalizeDemultiplexCounts.runtime_attr_override (RuntimeAttr?)
  • FinalizeDemultiplexReport.keyfile (File?)
  • FinalizeDemultiplexReport.runtime_attr_override (RuntimeAttr?)
  • FinalizeDemultiplexSummary.keyfile (File?)
  • FinalizeDemultiplexSummary.runtime_attr_override (RuntimeAttr?)
  • FinalizeLimaDetailedPNG.keyfile (File?)
  • FinalizeLimaDetailedPNG.runtime_attr_override (RuntimeAttr?)
  • FinalizeLimaSummary.keyfile (File?)
  • FinalizeLimaSummary.runtime_attr_override (RuntimeAttr?)
  • FinalizePbi.keyfile (File?)
  • FinalizePbi.runtime_attr_override (RuntimeAttr?)
  • IndexAlignedReads.runtime_attr_override (RuntimeAttr?)
  • IndexCCSUnalignedReads.runtime_attr_override (RuntimeAttr?)
  • MergeAllReads.runtime_attr_override (RuntimeAttr?)
  • MergeBarcodeBams.runtime_attr_override (RuntimeAttr?)
  • RefineTranscriptReads.runtime_attr_override (RuntimeAttr?)
  • SummarizedDemuxReportPNG.runtime_attr_override (RuntimeAttr?)

Defaults

  • drop_per_base_N_pulse_tags (Boolean, default=true)
  • ClusterTranscripts.use_qvs (Boolean, default=true)
  • CollapseTranscripts.use_qvs (Boolean, default=true)
  • Demultiplex.isoseq (Boolean, default=false)
  • Demultiplex.min_score (Int, default=0)
  • Demultiplex.peek (Int, default=0)
  • Demultiplex.peek_guess (Boolean, default=false)
  • RefineTranscriptReads.require_polya (Boolean, default=true)

Outputs

  • ccs_bam (File)
  • ccs_pbi (File)
  • aligned_bam (File)
  • aligned_bai (File)
  • aligned_pbi (File)
  • demux_counts (File)
  • demux_reports (File)
  • demux_summary (File)

Dot Diagram

PBCCSIsoSeq