LRConvertBCF

LRConvertBCF

description
Convert a BCF file into a .vcf.gz file. Meant to temporarily handle some transient issues stemming from the LRJointCallGVCFs workflow. Should be removed eventually.

Inputs

Required

  • gcs_out_root_dir (String, required): The root directory in GCS to store the output files
  • joint_bcf (File, required): The BCF file to convert
  • prefix (String, required): The prefix to use for the output files

Optional

  • ConcatBCFs.runtime_attr_override (RuntimeAttr?)
  • ConvertToHailMT.ref_fai (String?)
  • ConvertToHailMT.ref_fasta (String?)
  • ConvertToHailMT.runtime_attr_override (RuntimeAttr?)
  • FinalizeGVCF.keyfile (File?)
  • FinalizeGVCF.name (String?)
  • FinalizeGVCF.runtime_attr_override (RuntimeAttr?)
  • FinalizeHailMT.keyfile (File?)
  • FinalizeHailMT.name (String?)
  • FinalizeHailMT.runtime_attr_override (RuntimeAttr?)
  • FinalizeTBI.keyfile (File?)
  • FinalizeTBI.name (String?)
  • FinalizeTBI.runtime_attr_override (RuntimeAttr?)

Defaults

  • ConcatBCFs.is_gvcf (Boolean, default=false)
  • ConcatBCFs.num_cpus (Int, default=4)
  • ConvertToHailMT.reference (String, default="GRCh38")

Outputs

  • joint_vcf (File)
  • joint_vcf_tbi (File)
  • joint_mt (String)

Dot Diagram

LRConvertBCF