MalariaReportsWorkflow

GenerateMalariaReports

author
Bridget Knight
description

Report Generation

This workflow calls the Python script that generates a sequencing report.

Inputs

Required

  • aligned_bai (File, required): GCS path to aligned bai
  • aligned_bam (File, required): GCS path to aligned bam
  • aligned_bases (Float, required): total number of bases aligned to the reference genome
  • aligned_coverage (Float, required): number of reads uniquely mapped to a reference
  • aligned_reads (Int, required): total number of reads aligned to the reference genome
  • average_identity (Float, required)
  • fraction_aligned_bases (Float, required): number of bases aligned out of all bases in the sequence
  • location_table (File, required): table containing the region, district, site, and facility type for this sample's location
  • num_reads_q10 (Int, required): the number of reads where the probability of a given base call being wrong is 1 in 10
  • num_reads_q12 (Int, required): the number of reads where the probability of a given base call being wrong is approximately 1 in 16
  • num_reads_q15 (Int, required): the number of reads where the probability of a given base call being wrong is approximately 1 in 31
  • num_reads_q5 (Int, required): the number of reads where the probability of a given base call being wrong is approximately 1 in 3
  • num_reads_q7 (Int, required): the number of reads where the probability of a given base call being wrong is approximately 1 in 5
  • qc_pass (String, required): status to determine whether or not the sequencing run passes quality control standards
  • ref_map_file (File, required): table indicating reference sequence and auxillary file locations
  • regions_bed (File, required): GCS path to bed file containing drug resistance loci
  • sample_name (String, required): name of sequenced sample
  • tech_flag (String, required): string denoting if the sample was sequenced using long read or short read techniques
  • upload_date (String, required): date sample was uploaded

Optional

  • HRP2 (String?): value denoting whether the HRP2 marker is present or not -- true or false
  • HRP3 (String?): value denoting whether the HRP3 marker is present or not -- true or false
  • aligned_read_length (Float?): number at which 50% of the read lengths are longer than this value
  • barcode (String?): the barcode of the sample
  • code (String?): the three letter code denoting the corresponding health facility/site
  • collection_date (String?): date sample was collected
  • coverage_bin_size (Int?): number to use as size of bins for coverage plot generation; default is 1500
  • drug_resistance_text (File?): text file used for determining and displaying drug resistances
  • fastqc_path (File?): directory of fastqc_report used for finding BAM files
  • latitude (Float?): latitude value of where the sample was taken
  • location (String?): location where the sample was taken
  • longitude (Float?): longitude value of where the sample was taken
  • ont_qc_report (File?): ONT QC report file
  • pct_properly_paired_reads (Float?): percent of reads that are properly paired/aligned
  • read_qual_mean (Float?): mean measure of the uncertainty of base calls
  • sequencing_date (String?): date sample was sequenced
  • species (String?): species of sample
  • GenerateSnapshots.runtime_attr_override (RuntimeAttr?)
  • RunReportScript.runtime_attr_override (RuntimeAttr?)

Outputs

  • report (File)

Dot Diagram

MalariaReportsWorkflow