public void RunTask(string outputFolder, ISpritzParameters parameters, string displayName)
{
try
{
var stopWatch = new Stopwatch();
stopWatch.Start();
RunSpecific(parameters);
stopWatch.Stop();
var resultsFileName = Path.Combine(outputFolder, "results.txt");
using (StreamWriter file = new StreamWriter(resultsFileName))
{
file.WriteLine("Spritz: version ");
file.Write(stopWatch.Elapsed.ToString());
}
}
catch (Exception)
{
throw;
}
}
/// <summary>
/// Run this workflow (for GUI)
/// </summary>
/// <param name="parameters"></param>
protected override void RunSpecific(ISpritzParameters parameters)
{
Parameters = (AlignmentParameters)parameters;
PerformAlignment();
}
/// <summary>
/// Run this workflow (for GUI)
/// </summary>
/// <param name="parameters"></param>
protected override void RunSpecific(ISpritzParameters parameters)
{
Parameters = (GeneFusionDiscoveryParameters)parameters;
DiscoverGeneFusions();
}
/// <summary>
/// Run this workflow (for GUI)
/// </summary>
/// <param name="parameters"></param>
protected override void RunSpecific(ISpritzParameters parameters)
{
Parameters = (TranscriptQuantificationParameters)parameters;
QuantifyTranscripts();
}
protected abstract void RunSpecific(ISpritzParameters parameters);
/// <summary>
/// Run this workflow (for GUI)
/// </summary>
/// <param name="parameters"></param>
protected override void RunSpecific(ISpritzParameters parameters)
{
Parameters = (SampleSpecificProteinDBParameters)parameters;
GenerateSampleSpecificProteinDatabases();
}
/// <summary>
/// Run this workflow (for GUI)
/// </summary>
/// <param name="parameters"></param>
protected override void RunSpecific(ISpritzParameters parameters)
{
Parameters = (LncRNADiscoveryParameters)parameters;
LncRNADiscoveryFromFastqs();
}