PBUtils

GetRunInfo

description
Get run info from a PacBio BAM file.

Inputs

Required

  • SM (String, required): Sample name.
  • bam (String, required): BAM file.

Optional

  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Outputs

  • run_info (Map[String,String])
  • is_corrected (Boolean)

ShardLongReads

description
Shard long reads.

Inputs

Required

  • unaligned_bam (File, required): Unaligned BAM file.
  • unaligned_pbi (File, required): Unaligned BAM index file.

Optional

  • num_ssds (Int?): number of SSDs to use
  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Defaults

  • drop_per_base_N_pulse_tags (Boolean, default=false): Drop per-base N and pulse tags.
  • num_shards (Int, default=300): Number of shards.
  • num_threads (Int, default=8): Number of threads.
  • prefix (String, default="shard"): Prefix for shard BAM files.
  • zones (String, default="us-central1-c us-central1-b"): select which zone (GCP) to run this task

Outputs

  • unmapped_shards (Array[File])

CCS

description
Run CCS.

Inputs

Required

  • subreads (File, required): Subreads BAM file.

Optional

  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Defaults

  • all (Boolean, default=true): Generates one representative sequence per zero mode waveguide (ZMW), irrespective of quality and passes
  • by_strand (Boolean, default=false): Treats each strand of a ZMW (zero mode waveguide) as an individual entity and generates one consensus read for each strand that passes all filters.
  • kinetics (Boolean, default=false): Generate SQIIe values.

Outputs

  • consensus (File)
  • report (File)
  • report_json (File)
  • metrics_json (File)
  • hifi_summary_json (File)

ExtractHifiReads

description
Extract HiFi reads from a BAM file.

Inputs

Required

  • bam (File, required): Input BAM file.
  • library (String, required): Library name, this will override the LB: entry on the @RG line
  • sample_name (String, required): Sample name, we always rely explicitly on input SM name

Optional

  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Defaults

  • prefix (String, default="hifi"): Prefix for output files.

Outputs

  • hifi_bam (File)

MergeCCSReports

description
Merge CCS reports from shards of a single BAM.

Inputs

Required

  • reports (Array[File], required): Input CCS reports.

Optional

  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Defaults

  • prefix (String, default="out"): Prefix for output files.

Outputs

  • report (File)

Demultiplex

description
Demultiplex reads in a multiplexed PacBio bam.

Inputs

Required

  • bam (File, required): Input BAM.
  • barcode_file (File, required): Input barcode file.

Optional

  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Defaults

  • ccs (Boolean, default=false): Input BAM is CCS.
  • dump_removed (Boolean, default=false): Dump removed reads to a BAM file.
  • guess (Int, default=0): Guess barcodes.
  • guess_min_count (Int, default=0): Minimum number of reads to guess barcodes.
  • isoseq (Boolean, default=false): Input BAM is IsoSeq.
  • min_score (Int, default=0): Minimum barcode score.
  • peek (Int, default=0): Looks at the first n ZMWs of the input and return the mean
  • peek_guess (Boolean, default=false): Demultiplex Barcodes will run twice on the input data. For the first 50,000 ZMWs, it will guess the barcodes and store the mask of identified barcodes. In the second run, the barcode mask is used to demultiplex all ZMWs
  • prefix (String, default="demux"): Prefix for output files.
  • split_bam_named (Boolean, default=false): Split BAM by barcode name.

Outputs

  • demux_bams (Array[File])
  • counts (File)
  • report (File)
  • summary (File)
  • clips (File?)

MakeDetailedDemultiplexingReport

description
Make a detailed demultiplexing report.

Inputs

Required

  • report (File, required): Input report.

Optional

  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Defaults

  • type (String, default="png"): Output file type (pdf or png).

Outputs

  • report_files (Array[File])

MakeSummarizedDemultiplexingReport

description
Make a summarized demultiplexing report.

Inputs

Required

  • report (File, required): Input report.

Optional

  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Outputs

  • report_files (Array[File])

RefineTranscriptReads

description
Refine transcript reads.

Inputs

Required

  • bam (File, required): Input BAM file.
  • barcode_file (File, required): Input barcode file.

Optional

  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Defaults

  • prefix (String, default="flnc"): Prefix for output BAM file.
  • require_polya (Boolean, default=true): Require polyA tail.

Outputs

  • refined_bam (File)

ClusterTranscripts

description
Cluster transcripts.

Inputs

Required

  • bam (File, required): Input BAM file.

Optional

  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Defaults

  • prefix (String, default="clustered"): Prefix for output BAM file.
  • use_qvs (Boolean, default=true): Use CCS Analysis Quality Values.

Outputs

  • clustered_bam (File)
  • clustered_pbi (File)
  • hq_fasta (File)
  • hq_bam (File)
  • hq_pbi (File)
  • lq_fasta (File)
  • lq_bam (File)
  • lq_pbi (File)
  • cluster (File)
  • cluster_report_csv (File)
  • transcriptset_xml (File)

Align

description
Align reads to reference.

Inputs

Required

  • bam (File, required): Input BAM file.
  • drop_per_base_N_pulse_tags (Boolean, required): Drop per-base N and pulse tags.
  • map_preset (String, required)
  • ref_fasta (File, required): Input reference FASTA file.
  • sample_name (String, required): we always rely explicitly on input SM name

Optional

  • library (String?): this will override the LB: entry on the @RG line
  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Defaults

  • prefix (String, default="out"): Prefix for output BAM file.

Outputs

  • aligned_bam (File)
  • aligned_bai (File)

PBIndex

description
Index a BAM file.

Inputs

Required

  • bam (File, required): Input BAM file.

Optional

  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Outputs

  • pbi (File)

CollapseTranscripts

description
Collapse transcripts using isoseq3.

Inputs

Required

  • bam (File, required): Input BAM file.

Optional

  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Defaults

  • prefix (String, default="out"): Prefix for output files.
  • use_qvs (Boolean, default=true): Use CCS Analysis Quality Values.

Outputs

  • gff (File)

SummarizeCCSReport

description
Summarize CCS report.

Inputs

Required

  • report (File, required): Input CCS report.

Optional

  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Outputs

  • zmws_input (Float)
  • zmws_pass_filters (Float)
  • zmws_fail_filters (Float)
  • zmws_shortcut_filters (Float)
  • zmws_pass_filters_pct (Float)
  • zmws_fail_filters_pct (Float)
  • zmws_shortcut_filters_pct (Float)

SummarizePBI

description
Summarize PBI.

Inputs

Required

  • pbi (File, required): Input PBI.

Optional

  • runtime_attr_override (RuntimeAttr?): Override default runtime attributes.

Defaults

  • qual_threshold (Int, default=0): Quality threshold.

Outputs

  • results (Map[String,Float])