ONTProcessBasecall

ONTProcessBasecall

Inputs

Required

  • ID (String, required): the value to place in the BAM read group's ID field
  • SM (String, required): the value to place in the BAM read group's SM field
  • dir_prefix (String, required): directory prefix for output files
  • experiment_type (String, required): [default-valued] type of experiment run (DNA, RNA, R2C2)
  • gcs_out_root_dir (String, required): GCS bucket to store the reads, variants, and metrics files
  • ref_map_file (File, required): table indicating reference sequence and auxillary file locations

Optional

  • fastq_dir (String?): GCS path to fastq directory
  • final_summary (File?): GCS path to 'final_summary.txt*' file for basecalled fastq files
  • sequencing_summary (File?): GCS path to 'sequencing_summary.txt*' file for basecalled fastq files
  • AlignReads.library (String?)
  • AlignReads.runtime_attr_override (RuntimeAttr?)
  • ComputeGenomeLength.runtime_attr_override (RuntimeAttr?)
  • FinalizeAlignedBai.keyfile (File?)
  • FinalizeAlignedBai.name (String?)
  • FinalizeAlignedBai.runtime_attr_override (RuntimeAttr?)
  • FinalizeAlignedBam.keyfile (File?)
  • FinalizeAlignedBam.name (String?)
  • FinalizeAlignedBam.runtime_attr_override (RuntimeAttr?)
  • GetRunInfo.runtime_attr_override (RuntimeAttr?)
  • ListFastqs.runtime_attr_override (RuntimeAttr?)
  • ListFilesOfType.runtime_attr_override (RuntimeAttr?)
  • MergeAlignedReads.runtime_attr_override (RuntimeAttr?)
  • NanoPlotFromBam.runtime_attr_override (RuntimeAttr?)
  • NanoPlotFromRichFastqs.runtime_attr_override (RuntimeAttr?)
  • NanoPlotFromSummary.runtime_attr_override (RuntimeAttr?)
  • PartitionFastqManifest.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.AlignedFlagStats.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.AlignedReadMetrics.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageFullDist.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageFullDist.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageGlobalDist.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageGlobalDist.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageQuantized.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageQuantized.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageQuantizedCsi.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageQuantizedCsi.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageQuantizedDist.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageQuantizedDist.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageRegionDist.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageRegionDist.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageRegions.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageRegions.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageRegionsCsi.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageRegionsCsi.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFDepthSummaries.keyfile (File?)
  • PerFlowcellMetrics.FFDepthSummaries.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFYieldAligned.keyfile (File?)
  • PerFlowcellMetrics.FFYieldAligned.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.MakeChrIntervalList.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.MosDepth.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.MosDepth.window_size (Int?)
  • PerFlowcellMetrics.SummarizeDepth.runtime_attr_override (RuntimeAttr?)

Defaults

  • num_shards (Int, default=300): [default-valued] number of shards into which fastq files should be batched
  • AlignReads.prefix (String, default="out")
  • AlignReads.tags_to_preserve (Array[String], default=[])

Outputs

  • last_process_date (String)
  • aligned_bam (File)
  • aligned_bai (File)
  • raw_reads_stats (Map[String,Float])
  • aligned_reads_stats (Map[String,Float])

Dot Diagram

ONTProcessBasecall