AnnotateTranscriptomeWithGuide

AnnotateTranscriptomeWithGuide

description
Annotate a transcriptome with a guide GTF

Inputs

Required

  • aligned_bai (File, required): GCS path to aligned BAM file index
  • aligned_bam (File, required): GCS path to aligned BAM file
  • gcs_out_root_dir (String, required): GCS bucket to store the reads, variants, and metrics files
  • gtf (File, required): guide GTF (e.g. Gencode38)
  • participant_name (String, required): name of the participant from whom these samples were obtained
  • ref_map_file (File, required): table indicating reference sequence and auxillary file locations

Optional

  • CompareTranscriptomes.runtime_attr_override (RuntimeAttr?)
  • ExtractTranscriptSequences.runtime_attr_override (RuntimeAttr?)
  • FinalizeAnnotatedGTF.keyfile (File?)
  • FinalizeAnnotatedGTF.name (String?)
  • FinalizeAnnotatedGTF.runtime_attr_override (RuntimeAttr?)
  • FinalizeDict.keyfile (File?)
  • FinalizeDict.name (String?)
  • FinalizeDict.runtime_attr_override (RuntimeAttr?)
  • FinalizeFa.keyfile (File?)
  • FinalizeFa.name (String?)
  • FinalizeFa.runtime_attr_override (RuntimeAttr?)
  • FinalizeFai.keyfile (File?)
  • FinalizeFai.name (String?)
  • FinalizeFai.runtime_attr_override (RuntimeAttr?)
  • FinalizeGTF.keyfile (File?)
  • FinalizeGTF.name (String?)
  • FinalizeGTF.runtime_attr_override (RuntimeAttr?)
  • FinalizeLoci.keyfile (File?)
  • FinalizeLoci.name (String?)
  • FinalizeLoci.runtime_attr_override (RuntimeAttr?)
  • FinalizeRefMap.keyfile (File?)
  • FinalizeRefMap.name (String?)
  • FinalizeRefMap.runtime_attr_override (RuntimeAttr?)
  • FinalizeStats.keyfile (File?)
  • FinalizeStats.runtime_attr_override (RuntimeAttr?)
  • FinalizeTMap.keyfile (File?)
  • FinalizeTMap.name (String?)
  • FinalizeTMap.runtime_attr_override (RuntimeAttr?)
  • FinalizeTracking.keyfile (File?)
  • FinalizeTracking.name (String?)
  • FinalizeTracking.runtime_attr_override (RuntimeAttr?)
  • Quantify.runtime_attr_override (RuntimeAttr?)

Defaults

  • keep_retained_introns (Boolean, default=false): keep apparently retained introns in new transcriptome annotation

Outputs

  • transcriptome_gtf (File)
  • transcriptome_fa (File)
  • transcriptome_fai (File)
  • transcriptome_dict (File)
  • comp_annotated_gtf (File)
  • comp_loci (File)
  • comp_stats (File)
  • comp_tracking (File)
  • comp_refmap (File)
  • comp_tmap (File)

Dot Diagram

AnnotateTranscriptomeWithGuide