PfalciparumTypeDrugResistanceMarkers

PfalciparumTypeDrugResistanceMarkers

description
Workflow to generate a report of drug resistance markers

Inputs

Required

  • dir_prefix (String, required): Prefix for output directory
  • drug_resistance_list (File, required): List of drug resistance markers for which to search
  • ref_map_file (File, required): Table indicating reference sequence, auxillary file locations, and metadata.
  • snpeff_db (File, required): SnpEff database for functional annotation
  • vcf (File, required): VCF file to process
  • vcf_index (File, required): Index of the VCF file to process

Optional

  • gcs_out_root_dir (String?): GCS Bucket into which to finalize outputs. If no bucket is given, outputs will not be finalized and instead will remain in their native execution location.
  • CallDrugResistanceMutations.runtime_attr_override (RuntimeAttr?)
  • CreateDrugResistanceSummary.runtime_attr_override (RuntimeAttr?)
  • FinalizeAnnotatedVCF.keyfile (File?)
  • FinalizeAnnotatedVCF.name (String?)
  • FinalizeAnnotatedVCF.runtime_attr_override (RuntimeAttr?)
  • FinalizeAnnotatedVCFIndex.keyfile (File?)
  • FinalizeAnnotatedVCFIndex.name (String?)
  • FinalizeAnnotatedVCFIndex.runtime_attr_override (RuntimeAttr?)
  • FinalizeDRReport.keyfile (File?)
  • FinalizeDRReport.name (String?)
  • FinalizeDRReport.runtime_attr_override (RuntimeAttr?)
  • FinalizeDRSummary.keyfile (File?)
  • FinalizeDRSummary.name (String?)
  • FinalizeDRSummary.runtime_attr_override (RuntimeAttr?)
  • FinalizeSnpEffGenes.keyfile (File?)
  • FinalizeSnpEffGenes.name (String?)
  • FinalizeSnpEffGenes.runtime_attr_override (RuntimeAttr?)
  • FinalizeSnpEffSummary.keyfile (File?)
  • FinalizeSnpEffSummary.name (String?)
  • FinalizeSnpEffSummary.runtime_attr_override (RuntimeAttr?)
  • FunctionallyAnnotateVariants.runtime_attr_override (RuntimeAttr?)

Defaults

  • do_functional_annotation (Boolean, default=true): Whether to perform functional annotation

Outputs

  • drug_resistance_summary (File)
  • raw_drug_res_report (File)
  • predicted_drug_status_chloroquine (String)
  • predicted_drug_status_pyrimethamine (String)
  • predicted_drug_status_sulfadoxine (String)
  • predicted_drug_status_mefloquine (String)
  • predicted_drug_status_artemisinin (String)
  • predicted_drug_status_piperaquine (String)
  • annotated_vcf (File?)
  • annotated_vcf_index (File?)
  • snpEff_summary (File?)
  • snpEff_genes (File?)

Dot Diagram

PfalciparumTypeDrugResistanceMarkers