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approach 2 to issue #29 #52

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Jul 5, 2022
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approach 2 to issue #29 #52

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81fb872
approach 2 to issue #29
Jun 20, 2022
384ee25
added hla_typing_tumor subdir
Jun 28, 2022
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13 changes: 12 additions & 1 deletion definitions/immuno.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand All @@ -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
}
Expand Down