ONTFlowcellFromMultipleBasecalls

ONTFlowcellFromMultipleBasecalls

Inputs

Required

  • aligned_bais (Array[File], required)
  • aligned_bams (Array[File], required)
  • flowcell (String, required)
  • 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

  • bed_to_compute_coverage (File?): A BED listing regions where each will get a coverage summary
  • FinalizeAlignedBai.keyfile (File?)
  • FinalizeAlignedBai.name (String?)
  • FinalizeAlignedBai.runtime_attr_override (RuntimeAttr?)
  • FinalizeAlignedBam.keyfile (File?)
  • FinalizeAlignedBam.name (String?)
  • FinalizeAlignedBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeRegionalCoverage.keyfile (File?)
  • FinalizeRegionalCoverage.name (String?)
  • FinalizeRegionalCoverage.runtime_attr_override (RuntimeAttr?)
  • MergeAllReads.runtime_attr_override (RuntimeAttr?)
  • RemoveDuplicates.runtime_attr_override (RuntimeAttr?)
  • coverage.ComputeGenomeLength.runtime_attr_override (RuntimeAttr?)
  • coverage.MosDepthOverBed.runtime_attr_override (RuntimeAttr?)
  • coverage.NanoPlotFromBam.runtime_attr_override (RuntimeAttr?)
  • coverage.cov_over_region.runtime_attr_override (RuntimeAttr?)

Defaults

  • bams_suspected_to_contain_dup_record (Boolean, default=true): if the multiple basecalls are suspected to have duplicates amongst them

Outputs

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

Dot Diagram

ONTFlowcellFromMultipleBasecalls