Guppy

Guppy

description
Run Guppy basecaller on ONT FAST5 files. The docker tag number will match the version of Guppy that is being run. You can change this value to run a different version of Guppy. Currently supports... [3.5.2, 3.6.0, 4.0.14]. All fast5 files within the given GCS dir, gcs_fast5_dir, will be processed. Takes a few hours to process 130GB. Best guess is that the processing time scales linearly but untested.

Inputs

Required

  • config (String, required): Guppy config file.
  • gcs_fast5_dir (String, required): GCS path to a directory containing ONT FAST5 files.
  • gcs_out_root_dir (String, required): GCS path to a directory where the output will be written.

Optional

  • barcode_kit (String?): Optional. Barcode kit used for sequencing.
  • num_shards (Int?): Optional. Number of shards to use for parallelization. Default is 1 + ceil(length(read_lines(ListFast5s.manifest))/100).
  • protocol_run_id (String?): Optional. Protocol run ID used for sequencing. Default is 'unknown'.
  • sample_name (String?): Optional. Sample name used for sequencing. Default is 'unknown'.
  • Basecall.runtime_attr_override (RuntimeAttr?)
  • FinalizeBasecalls.runtime_attr_override (RuntimeAttr?)
  • ListFast5s.runtime_attr_override (RuntimeAttr?)
  • MakeFinalSummary.runtime_attr_override (RuntimeAttr?)
  • MakeSequencingSummary.runtime_attr_override (RuntimeAttr?)
  • PartitionFast5Manifest.runtime_attr_override (RuntimeAttr?)
  • SumFailingFastqs.runtime_attr_override (RuntimeAttr?)
  • SumPassingFastqs.runtime_attr_override (RuntimeAttr?)
  • TimestampStopped.runtime_attr_override (RuntimeAttr?)
  • UniqueBarcodes.runtime_attr_override (RuntimeAttr?)

Defaults

  • flow_cell_id (String, default="unknown"): Optional. Flow cell ID used for sequencing. Default is 'unknown'.
  • instrument (String, default="unknown"): Optional. Instrument used for sequencing. Default is 'unknown'.
  • Basecall.zones (String, default="us-central1-a us-central1-b us-central1-c us-central1-f")
  • SumFailingFastqs.prefix (String, default="sum")
  • SumPassingFastqs.prefix (String, default="sum")

Outputs

  • gcs_dir (String)
  • barcodes (Array[String])
  • num_fast5s (Int)
  • num_pass_fastqs (Int)
  • num_fail_fastqs (Int)

Dot Diagram

Guppy