public string GenerateSpritzCMDCommand(SpritzOptions options)
{
string command = $"conda run --no-capture-output --live-stream dotnet SpritzCMD.dll {SpritzOptionStrings.GenerateSpritzCMDArgs(options)}";
SpritzCMDCommand = command;
return(command);
}
public string GenerateSpritzCMDCommand(SpritzOptions options)
{
string command = $"/opt/conda/lib/dotnet/dotnet SpritzCMD.dll {SpritzOptionStrings.GenerateSpritzCMDArgs(options)}";
SpritzCMDCommand = command;
return(command);
}
public string GenerateSnakemakeCommand(SpritzOptions options, bool setup)
{
string cmd = "";
cmd += $"snakemake -j {options.Threads} --use-conda --conda-frontend mamba --configfile {Path.Combine(ConfigDirectory, "config.yaml")}";
if (setup)
{
cmd += " setup.txt";
}
SnakemakeCommand = cmd;
return(cmd);
}
public static string GenerateSpritzCMDArgs(SpritzOptions args)
{
// docker container working directory is /app/spritz/ and snakemake runs in /app/spritz/workflow/
// the results directory is /app/spritz/results/
string argsString =
$"--{ThreadsLong} {args.Threads} " +
$"--{AnalysisDirectoryLong}=/app/spritz/results/ ";
if (args.Reference != null && args.Reference != string.Empty)
{
argsString += $"--{ReferenceLong}=\"\"\"{args.Reference}\"\"\" ";
}
if (args.AnalyzeVariants)
{
argsString += $"--{AnalyzeVariantsLong} ";
}
if (args.AnalyzeIsoforms)
{
argsString += $"--{AnalyzeIsoformsLong} ";
}
if (args.Quantify)
{
argsString += $"--{QuantifyLong} ";
}
if (args.AvailableReferences)
{
argsString += $"--{AvailableReferencesLong} ";
}
if (args.Fastq1 != null && args.Fastq1 != string.Empty)
{
argsString += $"--{Fastq1Long}={args.Fastq1} ";
}
if (args.Fastq2 != null && args.Fastq2 != string.Empty)
{
argsString += $"--{Fastq2Long}={args.Fastq2} ";
}
if (args.Fastq1SingleEnd != null && args.Fastq1SingleEnd != string.Empty)
{
argsString += $"--{Fastq1SingleEndLong}={args.Fastq1SingleEnd} ";
}
if (args.SraAccession != null && args.SraAccession != string.Empty)
{
argsString += $"--{SraAccessionLong}={args.SraAccession} ";
}
if (args.SraAccessionSingleEnd != null && args.SraAccessionSingleEnd != string.Empty)
{
argsString += $"--{SraAccessionSingleEndLong}={args.SraAccessionSingleEnd} ";
}
return(argsString);
}
public void WriteConfig(SpritzOptions options, string analysisDirectoryStr)
{
const string initialContent = "---\nversion: 1\n"; // needed to start writing yaml file
var sr = new StringReader(initialContent);
var stream = new YamlStream();
stream.Load(sr);
var rootMappingNode = (YamlMappingNode)stream.Documents[0].RootNode;
var sras = options.SraAccession.Split(',');
var sras_se = options.SraAccessionSingleEnd.Split(',');
var fqs = options.Fastq1.Split(',') ?? Array.Empty <string>();
var fqs_se = options.Fastq1SingleEnd.Split(',') ?? Array.Empty <string>();
var analysisStrings = new List <string>();
if (options.AnalyzeVariants)
{
analysisStrings.Add("variant");
}
if (options.AnalyzeIsoforms)
{
analysisStrings.Add("isoform");
}
if (options.Quantify)
{
analysisStrings.Add("quant");
}
// write user input paired-end sras
YamlSequenceNode accession = new();
rootMappingNode.Add("sra", AddParam(sras, accession));
// write user input paired-end sras
YamlSequenceNode accession_se = new();
rootMappingNode.Add("sra_se", AddParam(sras_se, accession_se));
// write user input paired-end fastqs
YamlSequenceNode fq = new();
rootMappingNode.Add("fq", AddParam(fqs, fq));
// write user input paired-end fastqs
YamlSequenceNode fq_se = new();
rootMappingNode.Add("fq_se", AddParam(fqs_se, fq_se));
// write user defined analysis directory (input and output folder)
YamlSequenceNode analysisDirectory = new();
analysisDirectory.Style = SequenceStyle.Flow;
analysisDirectory.Add(analysisDirectoryStr);
rootMappingNode.Add("analysisDirectory", analysisDirectory);
// process reference string
var reference = options.Reference.Split(',');
if (reference.Length != 4)
{
throw new SpritzException($"Error: the reference string \"{reference}\" does not have four comma-separated elements corresponding to a line from genomes.csv.");
}
string releaseStr = reference[0];
string speciesStr = reference[1];
string organismStr = reference[2];
string referenceStr = reference[3];
// write ensembl release
YamlScalarNode release = new(releaseStr[8..]);