PfalciparumTypeDrugResistanceMarkers

PfalciparumTypeDrugResistanceMarkers

description
Workflow to generate a report of drug resistance markers

Inputs

Required

  • drug_resistance_list (File, required): List of drug resistance markers for which to search
  • gvcf (File, required): GVCF file to process to use for coverage analysis of drug resistance markers
  • gvcf_index (File, required): Index of the GVCF file to process
  • ref_map_file (File, required): Table indicating reference sequence, auxillary file locations, and metadata.
  • snpeff_db (File, required): SnpEff database for functional annotation
  • snpeff_db_identifier (String, required): Identifier for the SnpEff database to use
  • vcf (File, required): VCF file to process
  • vcf_index (File, required): Index of the VCF file to process

Optional

  • joint_vcfs (Array[File]?); description: Optional list of per-contig joint-call VCFs, given as paths/URLs (e.g. gs://...). When provided, the analyzed sample's resolved genotypes are STREAMED from these files at the drug-resistance loci and the files are never localized. Each must have a co-located tabix index (.tbi) and SnpEff (ANN) annotations, and the sample must be present in at least one of them or the workflow fails. The given GVCF is still used to fill in no-call evidence.; localization_optional: true
  • sample_id (String?): Optional sample ID to analyze when joint_vcfs is provided. Defaults to the single sample present in 'vcf'.
  • CallDrugResistanceMutations.runtime_attr_override (RuntimeAttr?)
  • CreateDrugResistanceSummary.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)
  • drug_resistance_markers (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?)
  • pfFd_Asp_193_Tyr (String)
  • pfaat1_Gln_454_Glu (String)
  • pfaat1_Lys_541_Asn (String)
  • pfaat1_Phe_313_Ser (String)
  • pfaat1_Ser_258_Leu (String)
  • pfap2_mu_Ile_592_Thr (String)
  • pfarps10_Val_127_Met (String)
  • pfatg18_Thr_38_Ile (String)
  • pfcarl_Ile_1139_Lys (String)
  • pfcarl_Leu_830_Val (String)
  • pfcarl_Ser_1076_Asn (String)
  • pfcarl_Ser_1076_Ile (String)
  • pfcarl_Val_1103_Leu (String)
  • pfcoronin_Arg_100_Lys (String)
  • pfcoronin_Glu_107_Val (String)
  • pfcoronin_Gly_50_Glu (String)
  • pfcoronin_Pro_76_Ser (String)
  • pfcrt_Asn_75_Glu (String)
  • pfcrt_Cys_101_Phe (String)
  • pfcrt_Cys_72_Ser (String)
  • pfcrt_Gly_353_Val (String)
  • pfcrt_His_97_Tyr (String)
  • pfcrt_Lys_76_Thr (String)
  • pfcrt_Met_343_Leu (String)
  • pfcrt_Met_74_Ile (String)
  • pfcrt_Phe_145_Ile (String)
  • pfcrt_Ser_350_Arg (String)
  • pfdhfr_Asn_51_Ile (String)
  • pfdhfr_Cys_50_Arg (String)
  • pfdhfr_Cys_59_Arg (String)
  • pfdhfr_Ile_164_Lys (String)
  • pfdhfr_Ser_108_Asn (String)
  • pfdhps_Ala_581_Gly (String)
  • pfdhps_Ala_613_Ser (String)
  • pfdhps_Ala_613_Thr (String)
  • pfdhps_Lys_437_Gly (String)
  • pfdhps_Lys_540_Glu (String)
  • pfdhps_Ser_436_Ala (String)
  • pfexo_Glu_415_Gly (String)
  • pfkelch13_Ala_675_Val (String)
  • pfkelch13_Arg_539_Thr (String)
  • pfkelch13_Arg_561_His (String)
  • pfkelch13_Arg_633_Ile (String)
  • pfkelch13_Asn_458_Tyr (String)
  • pfkelch13_Cys_580_Tyr (String)
  • pfkelch13_Ile_543_Thr (String)
  • pfkelch13_Met_476_Ile (String)
  • pfkelch13_Met_579_Ile (String)
  • pfkelch13_Phe_446_Ile (String)
  • pfkelch13_Phe_553_Leu (String)
  • pfkelch13_Phe_574_Leu (String)
  • pfkelch13_Phe_673_Ile (String)
  • pfkelch13_Pro_441_Ile (String)
  • pfkelch13_Pro_553_Leu (String)
  • pfkelch13_Pro_574_Leu (String)
  • pfkelch13_Tyr_493_His (String)
  • pfkelch13_Val_568_Gly (String)
  • pfmdr1_Asn_1024_Asp (String)
  • pfmdr1_Asn_86_Tyr (String)
  • pfmdr1_Asp_1246_Tyr (String)
  • pfmdr1_Ser_1034_Cys (String)
  • pfmdr1_Tyr_184_Phe (String)
  • pfmdr2_Thr_484_Ile (String)
  • pfubp1_Val_3275_Phe (String)

Dot Diagram

PfalciparumTypeDrugResistanceMarkers