diff --git a/definitions/immuno.wdl b/definitions/immuno.wdl index 69a14827..e929e983 100644 --- a/definitions/immuno.wdl +++ b/definitions/immuno.wdl @@ -13,6 +13,7 @@ import "tools/hla_consensus.wdl" as hc import "tools/intersect_known_variants.wdl" as ikv import "tools/pvacfuse.wdl" as pf import "types.wdl" # !UnusedImport +import "tools/optitype_dna.wdl" as od # # These structs are needed only because MiniWDL, used by some of our @@ -336,6 +337,15 @@ workflow immuno { optitype_name=optitype_name } + call od.optitypeDna as optitype { + input: + reference=reference, + reference_fai=reference_fai, + cram=somaticExome.tumor_cram, + cram_crai=somaticExome.tumor_cram_crai, + optitype_name=optitype_name + } + call pv.phaseVcf { input: somatic_vcf=somaticExome.final_filtered_vcf, @@ -585,7 +595,7 @@ workflow immuno { ] } - Array[File] hla_typing = flatten([ + Array[File] hla_typing_normal = flatten([ [germlineExome.optitype_tsv, germlineExome.optitype_plot, extractAlleles.allele_file, @@ -604,6 +614,7 @@ workflow immuno { File annotated_vcf = pvacseq.annotated_vcf File annotated_tsv = pvacseq.annotated_tsv + Array[File] hla_typing_tumor = optitype.optitype_tsv Array[File] pvacfuse_predictions = pvacfuse.pvacfuse_predictions Array[File] fusioninspector_evidence = rna.fusioninspector_evidence }