CollectPacBioAlignedMetrics

CollectPacBioAlignedMetrics

desciption
Collect a few custom metrics on the alignments.

Inputs

Required

  • aligned_bai (File, required)
  • aligned_bam (File, required)
  • aligned_pbi (File, required)

Optional

  • NanoPlotFromBam.runtime_attr_override (RuntimeAttr?)
  • SummarizeAlignedPBI.runtime_attr_override (RuntimeAttr?)
  • SummarizeAlignedQ10PBI.runtime_attr_override (RuntimeAttr?)
  • SummarizeAlignedQ12PBI.runtime_attr_override (RuntimeAttr?)
  • SummarizeAlignedQ15PBI.runtime_attr_override (RuntimeAttr?)
  • SummarizeAlignedQ5PBI.runtime_attr_override (RuntimeAttr?)
  • SummarizeAlignedQ7PBI.runtime_attr_override (RuntimeAttr?)

Defaults

  • SummarizeAlignedPBI.qual_threshold (Int, default=0)

Outputs

  • custom_aln_metrics_summary (File)
  • nanoplot_stats (File)
  • nanoplot_pngs (Array[File])

Dot Diagram

CollectPacBioAlignedMetrics