public SampleSet <CanvasEnrichmentOutput> Run(SampleSet <CanvasEnrichmentInput> inputs, IDirectoryLocation sandbox) { var targetedDbSnpVcfs = _enrichmentInputCreator.CreateDbSnpVcfForManifests(inputs, sandbox, _annotationFileProvider); var manifests = _enrichmentInputCreator.WriteManifests(inputs, sandbox); var outputs = new SampleSet <CanvasEnrichmentOutput>(); foreach (var input in inputs) { IDirectoryLocation sampleSandbox = sandbox.CreateSubdirectory(input.Key.Id); var dbSnpVcf = targetedDbSnpVcfs[input.Value.NexteraManifest]; var manifest = manifests[input.Value.NexteraManifest]; outputs.Add(input.Key, RunSingleSample(input.Key.Id, input.Value, dbSnpVcf, manifest, sampleSandbox)); } return(outputs); }
public SampleSet <CanvasOutput> Run(SampleSet <CanvasTumorNormalEnrichmentInput> inputs, IDirectoryLocation sandbox) { var bAlleleVcfs = GetBAlleleVcfs(inputs, sandbox); var manifests = _enrichmentInputCreator.WriteManifests(inputs, sandbox); var outputs = new SampleSet <CanvasOutput>(); foreach (var input in inputs) { IDirectoryLocation sampleSandbox = sandbox.CreateSubdirectory(input.Key.Id); var bAlleleVcf = bAlleleVcfs[input.Key].Item1; var isDbSnpVcf = bAlleleVcfs[input.Key].Item2; var manifest = manifests[input.Value.NexteraManifest]; outputs.Add(input.Key, RunSingleSample(input.Key.Id, input.Value, bAlleleVcf, isDbSnpVcf, manifest, sampleSandbox)); } return(outputs); }