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Commit 89b7851b authored by ffinfo's avatar ffinfo
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Added workaround for manta

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manta.wdl
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...@@ -72,10 +72,9 @@ task RunSomatic { ...@@ -72,10 +72,9 @@ task RunSomatic {
index: runDir + "/results/variants/tumorSV.vcf.gz.tbi" index: runDir + "/results/variants/tumorSV.vcf.gz.tbi"
} }
IndexedVcfFile? diploidSV = object { #FIXME: workaround for https://github.com/broadinstitute/cromwell/issues/4111
file: runDir + "/results/variants/diploidSV.vcf.gz", File? diploidSV = runDir + "/results/variants/diploidSV.vcf.gz"
index: runDir + "/results/variants/diploidSV.vcf.gz.tbi" File? diploidSVindex = runDir + "/results/variants/diploidSV.vcf.gz.tbi"
}
} }
runtime { runtime {
......
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