private CanvasOutput RunSingleSample(string sampleId, CanvasTumorNormalEnrichmentInput input, IFileLocation bAlleleVcf, bool isDbSnpVcf, IFileLocation manifest, IDirectoryLocation sampleSandbox)
{
if (!_annotationFileProvider.IsSupported(input.GenomeMetadata))
{
_logger.Info($"Skipping Canvas for sample {sampleId}: unsupported reference genome '{input.GenomeMetadata.Name}'");
return(null);
}
StringBuilder commandLine = new StringBuilder("Tumor-normal-enrichment");
commandLine.Append(_singleSampleInputCommandLineBuilder.GetSingleSampleCommandLine(sampleId, input.TumorBam, input.GenomeMetadata, sampleSandbox));
commandLine.Append($" --normal-bam \"{input.NormalBam.BamFile}\"");
commandLine.Append($" --manifest \"{manifest}\"");
var bAlleleVcfOptionName = isDbSnpVcf ?
SingleSampleCommonOptionsParser.PopulationBAlleleVcfOptionName :
SingleSampleCommonOptionsParser.SampleBAlleleVcfOptionName;
commandLine.Append($" --{bAlleleVcfOptionName} {bAlleleVcf.WrapWithShellQuote()}");
commandLine.Append($" --somatic-vcf \"{input.SomaticVcf.VcfFile}\"");
AddPloidyVcf(commandLine, SingleSampleCommonOptionsParser.PloidyVcfOptionName, input, sampleId, sampleSandbox);
commandLine.Append(_singleSampleInputCommandLineBuilder.GetCustomParameters());
commandLine = _singleSampleInputCommandLineBuilder.MergeCustomCanvasParameters(commandLine);
var job = new JobInfo(_runtimeExecutable.FullName, _canvasExe + " " + commandLine, "Canvas_" + sampleId);
return(_workDoer.DoWork(WorkResourceRequest.CreateExact(1, 8), job, GetCanvasOutput(sampleId, sampleSandbox)).Await());
}
public CanvasSmallPedigreeOutput Run(CanvasSmallPedigreeInput input, IDirectoryLocation sampleSandbox)
{
if (!_annotationFileProvider.IsSupported(input.GenomeMetadata))
{
_logger.Info($"Skipping Canvas: unsupported reference genome '{input.GenomeMetadata.Name}'");
return(null);
}
if (!_annotationFileProvider.CustomDbSnpVcf(input.GenomeMetadata) && input.Vcf == null)
{
_logger.Info($"Skipping Canvas. A dbSNP VCF file was not provided and no small variant VCF file is available");
return(null);
}
var commandLine = new StringBuilder("SmallPedigree-WGS");
commandLine.Append(GetMultiSampleCommandLine(input.Samples, input.GenomeMetadata, input.Vcf, sampleSandbox));
// use sample vcf by default (performance could be similar with dbSNP vcf though)
var bAlleleVcf = input.Vcf.VcfFile;
var bAlleleVcfOptionName = SingleSampleCommonOptionsParser.SampleBAlleleVcfOptionName;
if (_annotationFileProvider.CustomDbSnpVcf(input.GenomeMetadata))
{
bAlleleVcf = _annotationFileProvider.GetDbSnpVcf(input.GenomeMetadata);
bAlleleVcfOptionName = SingleSampleCommonOptionsParser.PopulationBAlleleVcfOptionName;
}
commandLine.Append($" --{bAlleleVcfOptionName} \"{bAlleleVcf}\"");
var ploidyInfos = input.Samples.SelectData(sample => sample.PloidyInfo);
var ploidyVcf = _canvasPloidyVcfCreator.CreatePloidyVcf(ploidyInfos, input.GenomeMetadata, sampleSandbox);
if (ploidyVcf != null)
{
commandLine.Append($" --{SmallPedigreeOptionsParser.PloidyVcfOptionName} \"{ploidyVcf.VcfFile}\"");
}
var moreCustomParameters = new Dictionary <string, string>();
// common cnv feature disabled by default due to CANV-397
// string canvasPedigreeCallerParam = $@"--commoncnvs {_annotationFileProvider.GetCanvasAnnotationFile(input.GenomeMetadata, "commoncnvs.bed")}";
// moreCustomParameters["CanvasPedigreeCaller"] = canvasPedigreeCallerParam;
commandLine.Append(_singleSampleInputCommandLineBuilder.GetCustomParameters(moreCustomParameters));
commandLine = _singleSampleInputCommandLineBuilder.MergeCustomCanvasParameters(commandLine);
// use Proband or, when proband is not available, first sample as pedigree id
var pedigreeId = input.Samples.Where(x => x.Value.SampleType == SampleType.Proband).Select(x => x.Key.Id).FirstOrDefault();
if (pedigreeId.IsNullOrEmpty())
{
pedigreeId = input.Samples.First().Key.Id;
}
var job = new JobInfo(_runtimeExecutable.FullName, _canvasExe + " " + commandLine, "Canvas_" + pedigreeId);
return(_workDoer.DoWork(WorkResourceRequest.CreateExact(1, 8), job, GetCanvasOutput(input.Samples, sampleSandbox)).Await());
}
private CanvasOutput RunSingleSample(string sampleId, CanvasTumorNormalWgsInput input, IDirectoryLocation sampleSandbox)
{
if (!_annotationFileProvider.IsSupported(input.GenomeMetadata))
{
_logger.Info($"Skipping Canvas for sample {sampleId}: unsupported reference genome '{input.GenomeMetadata.Name}'");
return(null);
}
StringBuilder commandLine = new StringBuilder("Somatic-WGS");
commandLine.Append(_singleSampleInputCommandLineBuilder.GetSingleSampleCommandLine(sampleId, input.TumorBam, input.GenomeMetadata, sampleSandbox));
commandLine.Append($" --{SingleSampleCommonOptionsParser.SampleBAlleleVcfOptionName} \"{input.NormalVcf.VcfFile}\"");
commandLine.Append($" --somatic-vcf \"{input.SomaticVcf.VcfFile}\"");
if (input.SexPloidy == null)
{
_logger.Warn("Sex chromosome ploidy not available. No ploidy will be provided to Canvas.");
}
else
{
_canvasPloidyVcfCreator.AddPloidyVcfOption(commandLine, SingleSampleCommonOptionsParser.PloidyVcfOptionName, input.GenomeMetadata, input.SexPloidy, sampleId, sampleSandbox);
}
commandLine.Append(_singleSampleInputCommandLineBuilder.GetCustomParameters());
commandLine = _singleSampleInputCommandLineBuilder.MergeCustomCanvasParameters(commandLine);
UnitOfWork singleSampleJob = new UnitOfWork()
{
ExecutablePath = _runtimeExecutable.FullName,
CommandLine = _canvasExe + " " + commandLine,
LoggingStub = "Canvas_" + sampleId,
};
var job = new JobInfo(_runtimeExecutable.FullName, _canvasExe + " " + commandLine, "Canvas_" + sampleId);
return(_workDoer.DoWork(WorkResourceRequest.CreateExact(1, 8), job, GetCanvasOutput(sampleId, sampleSandbox)).Await());
}
private CanvasEnrichmentOutput RunSingleSample(string sampleId, CanvasEnrichmentInput input, IFileLocation dbSnpVcf, IFileLocation manifest, IDirectoryLocation sampleSandbox)
{
if (!_annotationFileProvider.IsSupported(input.GenomeMetadata))
{
_logger.Info($"Skipping Canvas for sample {sampleId}: unsupported reference genome '{input.GenomeMetadata.Name}'");
return(null);
}
var moreCustomParameters = new Dictionary <string, string>();
StringBuilder commandLine = new StringBuilder("Somatic-Enrichment");
commandLine.Append(_singleSampleInputCommandLineBuilder.GetSingleSampleCommandLine(sampleId, input.Bam, input.GenomeMetadata, sampleSandbox));
string sexChromosomeKaryotype = null;
if (input.PloidyInfo.IsPloidyAvailable)
{
sexChromosomeKaryotype = input.PloidyInfo.IsXYMale.Value ? PloidyCorrector.PrettyPrintPloidy(1, 1)
: (input.PloidyInfo.IsXXFemale.Value ? PloidyCorrector.PrettyPrintPloidy(2, 0) : null);
}
string controlSexChromosomeKaryotype = null;
if (input.IsCanvasNormalizePcaMode && input.PloidyInfo.IsPloidyAvailable)
{
IFileLocation pcaModelFile = input.PloidyInfo.IsXYMale.Value ? input.PcaModels.MaleModelFile
: (input.PloidyInfo.IsXXFemale.Value ? input.PcaModels.FemaleModelFile : null);
if (pcaModelFile == null)
{
string sampleSex = input.PloidyInfo.IsXYMale.Value ? "male"
: (input.PloidyInfo.IsXXFemale.Value ? "female" : "sex unknown");
_logger.Info($"Skipping Canvas for sample {sampleId}: PCA model file not available for {sampleSex} samples.");
return(null);
}
moreCustomParameters["CanvasNormalize"] = "-m PCA";
commandLine.Append($" --control-binned \"{pcaModelFile}\"");
commandLine.Append($" --control-bin-size 100"); // use a dummy bin size for now
controlSexChromosomeKaryotype = sexChromosomeKaryotype;
}
else if (input.PrecomputedControl?.BinnedPath != null)
{
commandLine.Append($" --control-binned \"{input.PrecomputedControl.BinnedPath}\"");
commandLine.Append($" --control-bin-size {input.PrecomputedControl.BinSize}");
controlSexChromosomeKaryotype = input.PrecomputedControl.SexChromosomeKaryotype;
}
else
{
foreach (var normalBam in input.NormalBamPaths)
{
commandLine.Append($" --control-bam \"{normalBam.BamFile}\"");
}
}
AddControlPloidyVcf(commandLine, input, controlSexChromosomeKaryotype, sampleId, sampleSandbox);
commandLine.Append($" --{SingleSampleCommonOptionsParser.PopulationBAlleleVcfOptionName} \"{dbSnpVcf}\"");
commandLine.Append($" --manifest \"{manifest}\"");
AddSamplePloidyVcf(commandLine, input, sexChromosomeKaryotype, sampleId, sampleSandbox);
if (input.PredefinedBinsFile != null)
{
moreCustomParameters["CanvasBin"] = $"-n={input.PredefinedBinsFile.WrapWithEscapedShellQuote()}";
}
commandLine.Append(_singleSampleInputCommandLineBuilder.GetCustomParameters(moreCustomParameters));
commandLine = _singleSampleInputCommandLineBuilder.MergeCustomCanvasParameters(commandLine);
var job = new JobInfo(_runtimeExecutable.FullName, _canvasExe + " " + commandLine, "Canvas_" + sampleId);
return(_workDoer.DoWork(WorkResourceRequest.CreateExact(1, 8), job, GetCanvasOutput(sampleId, sampleSandbox)).Await());
}
