PanelProcessMalariaBarcodesForRh

PanelProcessMalariaBarcodesForRh

author
Jonn Smith
description
A workflow that processes P. falciparum SNP panels (read: barcodes) and calculates several metrics that are relevant to studying the epidemiology of the disease. This WDL calls a script written by Wes Wong and based on the following paper: https://doi.org/10.1093/pnasnexus/pgac187

Inputs

Required

  • A1 (Array[String], required): Nucleotide at the A1 barcode position.
  • A10 (Array[String], required): Nucleotide at the A10 barcode position.
  • A11 (Array[String], required): Nucleotide at the A11 barcode position.
  • A12 (Array[String], required): Nucleotide at the A12 barcode position.
  • A2 (Array[String], required): Nucleotide at the A2 barcode position.
  • A3 (Array[String], required): Nucleotide at the A3 barcode position.
  • A4 (Array[String], required): Nucleotide at the A4 barcode position.
  • A5 (Array[String], required): Nucleotide at the A5 barcode position.
  • A6 (Array[String], required): Nucleotide at the A6 barcode position.
  • A7 (Array[String], required): Nucleotide at the A7 barcode position.
  • A8 (Array[String], required): Nucleotide at the A8 barcode position.
  • A9 (Array[String], required): Nucleotide at the A9 barcode position.
  • Adjusted_Het (Array[String], required)
  • B1 (Array[String], required): Nucleotide at the B1 barcode position.
  • B10 (Array[String], required): Nucleotide at the B10 barcode position.
  • B11 (Array[String], required): Nucleotide at the B11 barcode position.
  • B12 (Array[String], required): Nucleotide at the B12 barcode position.
  • B2 (Array[String], required): Nucleotide at the B2 barcode position.
  • B3 (Array[String], required): Nucleotide at the B3 barcode position.
  • B4 (Array[String], required): Nucleotide at the B4 barcode position.
  • B5 (Array[String], required): Nucleotide at the B5 barcode position.
  • B6 (Array[String], required): Nucleotide at the B6 barcode position.
  • B7 (Array[String], required): Nucleotide at the B7 barcode position.
  • B8 (Array[String], required): Nucleotide at the B8 barcode position.
  • B9 (Array[String], required): Nucleotide at the B9 barcode position.
  • Barcode_String (Array[String], required): Nucleotide sequence of all barcode SNPs in genomic order.
  • Delta_CT_Threshold (Array[String], required)
  • ISO3 (Array[String], required)
  • M_P (Array[String], required): Mono- / Poly-clonal indicator.
  • N (Array[String], required)
  • Number_Text (Array[String], required)
  • Raw_Name (Array[String], required)
  • Sample_Name (Array[String], required)
  • X (Array[String], required)
  • Year (Array[String], required): Year this dataset was collected.
  • barcode_def_tsv (File, required): TSV file containing the definition of the SNP barcode sites with the columns: Name, Contig, Position
  • cc (Array[String], required)
  • dir_prefix (String, required): directory prefix for output files
  • gcs_out_root_dir (String, required): GCS bucket to store the reads, variants, and metrics files
  • location_code (String, required): Location code of the sample. Should correspond to the ISO3 value.
  • mccoil_median (Array[String], required)

Optional

  • t_002_ProcessBarcodeSpreadsheet.runtime_attr_override (RuntimeAttr?)
  • t_003_FinalizeOutputs.runtime_attr_override (RuntimeAttr?)

Defaults

  • DEBUG_MODE (Boolean, default=false)
  • t_001_WdlExecutionStartTimestamp.date_format (String, default="%Y%m%d_%H%M%S_%N")

Outputs

  • summary_figure_svg (File)
  • summary_figure_png (File)
  • summary_stats (File)
  • mono_barcode_stats (File)
  • poly_barcode_stats (File)
  • input_tsv (File)

Dot Diagram

PanelProcessMalariaBarcodesForRh