public SampleSet <CanvasOutput> Run(SampleSet <CanvasTumorNormalWgsInput> inputs, IDirectoryLocation sandbox)
{
var outputs = new SampleSet <CanvasOutput>();
foreach (var input in inputs)
{
IDirectoryLocation sampleSandbox = sandbox.CreateSubdirectory(input.Key.Id);
outputs.Add(input.Key, RunSingleSample(input.Key.Id, input.Value, sampleSandbox));
}
return(outputs);
}
public IFileLocation Write(IReadOnlyList <CanvasSegment> segments, IDirectoryLocation output,
double normalizationFactor)
{
_logger.Info($"Begin writing bedgraph file at '{output}'");
var benchmark = new Benchmark();
var bedGraph = output.GetFileLocation("coverage.bedgraph");
_writer.Write(segments, bedGraph, normalizationFactor);
_logger.Info($"Finished writing bedgraph file at '{bedGraph}'. Elapsed time: {benchmark.GetElapsedTime()}");
_logger.Info($"Begin conversion of '{bedGraph}' to bigwig file");
benchmark = new Benchmark();
var bigWigConverterOutput = output.CreateSubdirectory("BigWigConverter");
var bigwigFile = _converter.Convert(bedGraph, _genome, bigWigConverterOutput);
if (bigwigFile != null)
{
_logger.Info(
$"Finished conversion from bedgraph file at '{bedGraph}' to bigwig file at '{bigwigFile}'. Elapsed time: {benchmark.GetElapsedTime()}");
}
return(bigwigFile);
}
public int Launch()
{
CommonOptions commonOptions = _modeRunner.CommonOptions;
IDirectoryLocation outFolder = commonOptions.OutputDirectory;
var log = outFolder.GetFileLocation("CanvasLog.txt");
var error = outFolder.GetFileLocation("CanvasError.txt");
using (ILogger logger = new Logger(log, error))
{
try
{
logger.Info($"Running Canvas {_mode} {_version}");
logger.Info($"Command-line arguments: {string.Join(" ", _args)}");
var checkpointRunner =
GetCheckpointRunner(
logger,
outFolder,
commonOptions.StartCheckpoint,
commonOptions.StopCheckpoint,
commonOptions.WholeGenomeFasta);
using (var manager = checkpointRunner.Manager)
{
IDirectoryLocation loggingFolder = outFolder.CreateSubdirectory("Logging");
IsasConfiguration config = IsasConfiguration.GetConfiguration();
IWorkManager workManager = new LocalWorkManager(logger, loggingFolder, 0, config.MaximumMemoryGB, config.MaximumHoursPerProcess);
_modeRunner.Run(logger, checkpointRunner, workManager);
manager.CheckFinalState();
}
}
catch (StopCheckpointFoundException) { }
catch (Exception e)
{
logger.Error($"Canvas workflow error: {e}");
return(-1);
}
}
return(0);
}
private void AddControlPloidyVcf(StringBuilder commandLine, CanvasEnrichmentInput input, string SexChromosomeKaryotype, string sampleId, IDirectoryLocation sampleSandbox)
{
if (SexChromosomeKaryotype == null)
{
_logger.Warn("Sex chromosome ploidy not available for control sample. No ploidy will be provided to Canvas.");
return;
}
_canvasPloidyVcfCreator.AddPloidyVcfOption(commandLine, SomaticEnrichmentOptionsParser.ControlPloidyVcfOptionName, input.GenomeMetadata, SexPloidyInfo.FromKaryotype(SexChromosomeKaryotype), sampleId, sampleSandbox.CreateSubdirectory("control"));
}
/// <summary>
/// Copy a directory into some parent directory.
/// If a directory with the same name exists in the parent directory it is first removed.
/// Returns the copied directory
/// </summary>
public IDirectoryLocation CopyInto(IDirectoryLocation parentDirectoryLocation)
{
return CopyTo(parentDirectoryLocation.CreateSubdirectory(Name));
}
/// <summary>
/// Moves a directory into a parent directory. If paths are not on the same filesystem volume this is equivalent to CopyInto() then Delete()
/// If the parentDirectoryLocation already contains a directory with the same it is first removed
/// Returns the directory in its new location
/// </summary>
public IDirectoryLocation MoveInto(IDirectoryLocation parentDirectoryLocation)
{
return MoveTo(parentDirectoryLocation.CreateSubdirectory(Name));
}
public static IDirectoryLocation GetFastqFolder(IDirectoryLocation analysisFolder)
{
return analysisFolder.CreateSubdirectory(FastqFolderName);
}
public static IDirectoryLocation GetLoggingFolder(IDirectoryLocation analysisFolder)
{
return analysisFolder.CreateSubdirectory(LoggingFolderName);
}
public static IDirectoryLocation GetCheckpointFolder(IDirectoryLocation analysisFolder)
{
return analysisFolder.CreateSubdirectory(CheckpointFolderName);
}