ONTMethylation

ONTMethylation

description
ONT Methylation pipeline

Inputs

Required

  • gcs_fast5_dir (String, required): GCS directory containing fast5 files
  • gcs_out_root_dir (String, required): GCS directory to write output files
  • participant_name (String, required): Participant name
  • prefix (String, required): Prefix for output files
  • ref_map_file (File, required): Reference map file
  • variants (File, required): VCF file containing variants
  • variants_tbi (File, required): Tabix index for VCF file

Optional

  • CallHaplotype1Variants.runtime_attr_override (RuntimeAttr?)
  • CallHaplotype2Variants.runtime_attr_override (RuntimeAttr?)
  • CatMappingSummaries.runtime_attr_override (RuntimeAttr?)
  • CatModifiedBases5mC.runtime_attr_override (RuntimeAttr?)
  • CatSequencingSummaries.runtime_attr_override (RuntimeAttr?)
  • ChunkManifest.runtime_attr_override (RuntimeAttr?)
  • ExtractHaplotypeReads.runtime_attr_override (RuntimeAttr?)
  • FinalizeHaplotaggedBai.keyfile (File?)
  • FinalizeHaplotaggedBai.runtime_attr_override (RuntimeAttr?)
  • FinalizeHaplotaggedBam.keyfile (File?)
  • FinalizeHaplotaggedBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeHaplotype1Tbi.keyfile (File?)
  • FinalizeHaplotype1Tbi.runtime_attr_override (RuntimeAttr?)
  • FinalizeHaplotype1Vcf.keyfile (File?)
  • FinalizeHaplotype1Vcf.runtime_attr_override (RuntimeAttr?)
  • FinalizeHaplotype2Tbi.keyfile (File?)
  • FinalizeHaplotype2Tbi.runtime_attr_override (RuntimeAttr?)
  • FinalizeHaplotype2Vcf.keyfile (File?)
  • FinalizeHaplotype2Vcf.runtime_attr_override (RuntimeAttr?)
  • FinalizeModMappedBai.keyfile (File?)
  • FinalizeModMappedBai.runtime_attr_override (RuntimeAttr?)
  • FinalizeModMappedBam.keyfile (File?)
  • FinalizeModMappedBam.runtime_attr_override (RuntimeAttr?)
  • FinalizePhasedTbi.keyfile (File?)
  • FinalizePhasedTbi.runtime_attr_override (RuntimeAttr?)
  • FinalizePhasedVcf.keyfile (File?)
  • FinalizePhasedVcf.runtime_attr_override (RuntimeAttr?)
  • Haplotag.runtime_attr_override (RuntimeAttr?)
  • IndexVariants.runtime_attr_override (RuntimeAttr?)
  • ListFilesOfType.runtime_attr_override (RuntimeAttr?)
  • MakeChrIntervalList.runtime_attr_override (RuntimeAttr?)
  • Megalodon.runtime_attr_override (RuntimeAttr?)
  • MergeFastqs.runtime_attr_override (RuntimeAttr?)
  • MergeHaplotagBams.runtime_attr_override (RuntimeAttr?)
  • MergeMappings.runtime_attr_override (RuntimeAttr?)
  • MergeModMappings.runtime_attr_override (RuntimeAttr?)
  • MergeModifiedBaseCallDBs.runtime_attr_override (RuntimeAttr?)
  • MergePerChrCalls.runtime_attr_override (RuntimeAttr?)
  • MergeVarMappings.runtime_attr_override (RuntimeAttr?)
  • MergeVariantDBs.runtime_attr_override (RuntimeAttr?)
  • PhaseVariants.runtime_attr_override (RuntimeAttr?)
  • SubsetBam.runtime_attr_override (RuntimeAttr?)
  • SubsetVCF.runtime_attr_override (RuntimeAttr?)
  • WhatsHapFilter.runtime_attr_override (RuntimeAttr?)

Defaults

  • ListFilesOfType.recurse (Boolean, default=false)
  • Megalodon.zones (String, default="us-central1-a us-central1-b us-central1-c us-central1-f")
  • MergeHaplotagBams.prefix (String, default="out"): Prefix for output files
  • MergeMappings.prefix (String, default="out"): Prefix for output files
  • MergeModMappings.prefix (String, default="out"): Prefix for output files
  • MergeVarMappings.prefix (String, default="out"): Prefix for output files

Outputs

  • phased_vcf (File)
  • phased_tbi (File)
  • mod_mapped_bam (File)
  • mod_mapped_bai (File)
  • haplotagged_bam (File)
  • haplotagged_bai (File)
  • haplotype1_vcf (File)
  • haplotype1_tbi (File)
  • haplotype2_vcf (File)
  • haplotype2_tbi (File)

Dot Diagram

ONTMethylation