public InRunTask(string displayName, SpritzOptions options) : base(displayName, displayName)
{
this.options = options;
}
public PreRunTask(SpritzOptions options)
{
this.options = options;
}
private static void Main(string[] args)
{
Console.WriteLine("Welcome to Spritz!");
FluentCommandLineParser <SpritzOptions> p = new();
// Get defaults
SpritzOptions defaults = new();
defaults.AnalysisDirectory = SpritzOptions.DefaultAnalysisDirectory();
defaults.Threads = Environment.ProcessorCount;
p.Setup(arg => arg.AnalysisDirectory)
.As(SpritzOptionStrings.AnalysisDirectoryShort,
SpritzOptionStrings.AnalysisDirectoryLong)
.SetDefault(defaults.AnalysisDirectory)
.WithDescription(SpritzOptionStrings.AnalysisDirectoryDesc);
p.Setup(arg => arg.AnalyzeVariants)
.As(SpritzOptionStrings.AnalyzeVariantsShort,
SpritzOptionStrings.AnalyzeVariantsLong)
.SetDefault(defaults.AnalyzeVariants)
.WithDescription(SpritzOptionStrings.AnalyzeVariantsDesc);
p.Setup(arg => arg.AnalyzeIsoforms)
.As(SpritzOptionStrings.AnalyzeIsoformsShort,
SpritzOptionStrings.AnalyzeIsoformsLong)
.SetDefault(defaults.AnalyzeIsoforms)
.WithDescription(SpritzOptionStrings.AnalyzeIsoformsDesc);
p.Setup(arg => arg.Quantify)
.As(SpritzOptionStrings.QuantifyShort,
SpritzOptionStrings.QuantifyLong)
.SetDefault(defaults.Quantify)
.WithDescription(SpritzOptionStrings.QuantifyDesc);
p.Setup(arg => arg.AvailableReferences)
.As(SpritzOptionStrings.AvailableReferencesShort,
SpritzOptionStrings.AvailableReferencesLong)
.SetDefault(false)
.WithDescription(SpritzOptionStrings.AvailableReferencesDesc);
p.Setup(arg => arg.AnalysisSetup)
.As(SpritzOptionStrings.AnalysisSetupShort,
SpritzOptionStrings.AnalysisSetupLong)
.SetDefault(false)
.WithDescription(SpritzOptionStrings.AnalysisSetupDesc);
p.Setup(arg => arg.Fastq1)
.As(SpritzOptionStrings.Fastq1Short,
SpritzOptionStrings.Fastq1Long)
.WithDescription(SpritzOptionStrings.Fastq1Desc);
p.Setup(arg => arg.Fastq2)
.As(SpritzOptionStrings.Fastq2Short,
SpritzOptionStrings.Fastq2Long)
.WithDescription(SpritzOptionStrings.Fastq2Desc);
p.Setup(arg => arg.Fastq1SingleEnd)
.As(SpritzOptionStrings.Fastq1SingleEndShort,
SpritzOptionStrings.Fastq1SingleEndLong)
.WithDescription(SpritzOptionStrings.Fastq1SingleEndDesc);
p.Setup(arg => arg.SraAccession)
.As(SpritzOptionStrings.SraAccessionShort,
SpritzOptionStrings.SraAccessionLong)
.WithDescription(SpritzOptionStrings.SraAccessionDesc);
p.Setup(arg => arg.SraAccessionSingleEnd)
.As(SpritzOptionStrings.SraAccessionSingleEndShort,
SpritzOptionStrings.SraAccessionSingleEndLong)
.WithDescription(SpritzOptionStrings.SraAccessionSingleEndDesc);
p.Setup(arg => arg.Threads)
.As(SpritzOptionStrings.ThreadsShort,
SpritzOptionStrings.ThreadsLong)
.SetDefault(defaults.Threads)
.WithDescription(SpritzOptionStrings.ThreadsDesc);
p.Setup(arg => arg.Reference)
.As(SpritzOptionStrings.ReferenceShort,
SpritzOptionStrings.ReferenceLong)
.WithDescription(SpritzOptionStrings.ReferenceDesc);
string helpoutro = "";
helpoutro += $"The Spritz commandline interface intended to be run within a conda environment containing the programs snakemake and mamba." + Environment.NewLine;
helpoutro += Environment.NewLine;
helpoutro += $"Example workflow using this tool:" + Environment.NewLine;
helpoutro += $"1) Check out the available references with the -x command. Specify a target directory with -a." + Environment.NewLine;
helpoutro += $"2) Run spritz with -r based on the genomes.csv file generated by 1), " + Environment.NewLine;
helpoutro += $"and choose the workflow options -b to analyze variants, -c to analyze isoforms, or both, and results will be saved at directory specified by -a. " + Environment.NewLine;
helpoutro += $"2b) Alternatively, specify false for both -v and -w to generate a reference proteogenomic database from the Ensembl references." + Environment.NewLine;
helpoutro += Environment.NewLine;
p.SetupHelp("h", "help")
.Callback(text => Console.WriteLine(text + helpoutro));
var result = p.Parse(args);
// handle unrecognized and unmatched
bool anyUnrecognized = result.AdditionalOptionsFound.Any();
int countUnmatched = result.UnMatchedOptions.Count();
var possibleMatches = typeof(SpritzOptions).GetFields(BindingFlags.Instance | BindingFlags.Static | BindingFlags.NonPublic | BindingFlags.NonPublic);
if (anyUnrecognized)
{
throw new SpritzException($"Error: unrecognized commandline argument(s): {string.Join(',', result.AdditionalOptionsFound.Select(x => x.ToString()))}");
}
else if (countUnmatched == possibleMatches.Length)
{
result = p.Parse(new[] { "-h" });
}
string analysisDirectory = RunnerEngine.TrimQuotesOrNull(p.Object.AnalysisDirectory);
Console.WriteLine($"Testing analysis directory {analysisDirectory}");
if (!RunnerEngine.IsDirectoryWritable(analysisDirectory))
{
analysisDirectory = Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.UserProfile), "spritz", "results");
}
Console.WriteLine($"Using analysis directory {analysisDirectory}");
Console.WriteLine();
bool noSequencesSpecified =
p.Object.SraAccession == null && p.Object.SraAccessionSingleEnd == null &&
p.Object.Fastq1 == null && p.Object.Fastq1SingleEnd == null && p.Object.Fastq2 == null;
bool analysisSpecified =
p.Object.AnalyzeVariants || p.Object.AnalyzeIsoforms || p.Object.Quantify;
if (result.HelpCalled)
{
return;
}
else if (p.Object.AvailableReferences)
{
Console.WriteLine();
Console.WriteLine($"Saving the list of available references to {Path.Combine(analysisDirectory, "genomes.csv")}.");
string genomesPath = Path.Combine(Directory.GetCurrentDirectory(), "genomes.csv");
Directory.CreateDirectory(analysisDirectory);
string dest = Path.Combine(analysisDirectory, Path.GetFileName(genomesPath));
if (File.Exists(dest))
{
Console.WriteLine($"File {dest} already exists. Please check it out there.");
}
else
{
File.Copy(genomesPath, dest);
}
return;
}
else if (p.Object.Reference == null)
{
throw new SpritzException("Error: No reference specified. Please specify one with the -r flag that has four elements corresponding to a line from genomes.csv.");
}
else if (analysisSpecified && noSequencesSpecified)
{
throw new SpritzException("Error: An analysis was specified, but no sequences were specified to analyze. Please try again after specifying fastqs or sras.");
}
else
{
if (!analysisSpecified && noSequencesSpecified)
{
Console.WriteLine("NB: No sequences or analyses were specified, and so a reference database will be generated from Ensembl references only.");
}
SpritzOptions options = CleanOptions(p.Object, analysisDirectory);
RunnerEngine runner = new(new("", options), analysisDirectory);
runner.WriteConfig(options, analysisDirectory);
runner.GenerateSnakemakeCommand(options, p.Object.AnalysisSetup);
string snakemakeArguments = runner.SnakemakeCommand["snakemake ".Length..];
