CCSPepper

CCSPepper

description
Workflow for getting haplotagged BAM, VCF and gVCF from DV-pepper. Note VCF is un-phased.

Inputs

Required

  • bai (File, required): Input BAM index file
  • bam (File, required): Input BAM file
  • dv_memory (Int, required): Memory for DeepVariant
  • dv_threads (Int, required): Number of threads for DeepVariant
  • pepper_memory (Int, required): Memory for Pepper
  • pepper_threads (Int, required): Number of threads for Pepper
  • ref_fasta (File, required): Reference fasta file
  • ref_fasta_fai (File, required): Reference fasta index file

Optional

  • deep_variant.runtime_attr_override (RuntimeAttr?)
  • get_hap_tagged_bam.runtime_attr_override (RuntimeAttr?)

Defaults

  • zones (String, default="us-central1-b us-central1-c"): select which zone (GCP) to run this task

Outputs

  • VCF (File)
  • VCF_tbi (File)
  • gVCF (File)
  • gVCF_tbi (File)
  • hap_tagged_bam (File)
  • hap_tagged_bai (File)

Dot Diagram

CCSPepper