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
• predicted_drug_status_artemisinin (String?): value denoting the sensitivity of this sample to artemisinin
• predicted_drug_status_chloroquine (String?): value denoting the sensitivity of this sample to chloroquine
• predicted_drug_status_mefloquine (String?): value denoting the sensitivity of this sample to mefloquine
• predicted_drug_status_piperaquine (String?): value denoting the sensitivity of this sample to piperaquine
• predicted_drug_status_pyrimethamine (String?): value denoting the sensitivity of this sample to pyrimethamine
• predicted_drug_status_sulfadoxine (String?): value denoting the sensitivity of this sample to sulfadoxine
• 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