PfalciparumPolygenomicityBarcodeEstimate

PfalciparumPolygenomicityBarcodeEstimate

author
Jonn Smith
description
This workflow estimates whether a given sample is polygenomic or monogenomic based on a given fingerprint / barcode. Fingerprint is assumed to be 24 SNP barcode from Daniels et al. If no fingerprint / barcode is given, the fingerprint will be extracted from the given VCF.

Inputs

Required

  • sample_name (String, required): Name of the sample to be processed.

Optional

  • barcode_string (String?): Barcode to use for genomicity estimation. Assumed to be 24 SNP barcode from Daniels et al.
  • fingerprint_haploytpe_db_file (File?): Haplotype DB file from which to fingerprint the input data.
  • ref_map_file (String?): Reference map file indicating reference sequence and auxillary file locations.
  • vcf (File?): VCF file from which to extract the barcode.
  • vcf_index (File?): Index for the VCF file.
  • t_001_FingerprintAndBarcodeVcf.runtime_attr_override (RuntimeAttr?)
  • t_002_EstimateGenomicityFromBarcode.runtime_attr_override (RuntimeAttr?)

Defaults

  • t_002_EstimateGenomicityFromBarcode.hets_for_poly (Int, default=2)

Outputs

  • genomicity (String)
  • fingerprint_vcf (File?)
  • barcode (String?)

Dot Diagram

PfalciparumPolygenomicityBarcodeEstimate