ExpandedDrugResistanceMarkerExtraction

ExpandedDrugResistanceMarkerExtraction

author
Jonn Smith
description
Extract drug resistance marker information from a single-sample VCF.

Inputs

Required

  • dir_prefix (String, required): Directory prefix to use for finalized location.
  • gcs_out_root_dir (String, required): GCS Bucket into which to finalize outputs.
  • gene_drug_resistance_list (File, required): List of genes over which to include any variants in the expanded drug resistance report.
  • protein_drug_resistance_list (File, required): List of specific protein changes to include in the expanded drug resistance report.
  • sample_name (String, required): Name of the sample in the given single-sample VCF file.
  • snpeff_db (File, required): SNPEff database file to use for functional annotations (if necessary).
  • vcf (File, required): Input VCF.gz file containing variant calls from which to create an expanded drug resistance marker report.

Optional

  • CallDrugResistanceMutations.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?)
  • FinalizeDRReportAllMarkers.keyfile (File?)
  • FinalizeDRReportAllMarkers.name (String?)
  • FinalizeDRReportAllMarkers.runtime_attr_override (RuntimeAttr?)
  • FinalizeDRReportProteinMarkers.keyfile (File?)
  • FinalizeDRReportProteinMarkers.name (String?)
  • FinalizeDRReportProteinMarkers.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): If true, will perform functional annotation on the input VCF file prior to extracting drug resistance marker information.

Outputs

  • drug_res_report_all (File)
  • drug_res_report_prot_only (File)
  • annotated_vcf (File?)
  • annotated_vcf_index (File?)
  • snpEff_summary (File?)
  • snpEff_genes (File?)

Dot Diagram

ExpandedDrugResistanceMarkerExtraction