public override async Task <ExecutionResult> RunAsync(IStepExecutionContext context) { if (DownloadUrl == null) { throw new Exception("Can't download, url missing"); } Output = Session.CreateFolder().CreateFile(FileName); using (var client = new WebClient()) { client.DownloadProgressChanged += (_, e) => { EventManager.ReportStepProgress(context, e.ProgressPercentage); }; await client.DownloadFileTaskAsync(DownloadUrl, Output.AbsolutePath); } return(ExecutionResult.Next()); }
public override async Task <ExecutionResult> RunAsync(IStepExecutionContext context) { var ouput = Session.CreateFolder(); Output1 = ouput.GetFile("output_1.fastq"); Output2 = ouput.GetFile("output_2.fastq"); var command = Cli .Wrap("fastp") .WithArguments(args => args .Add("-i") .Add(Fastq1.AbsolutePath) .Add("-I") .Add(Fastq1.AbsolutePath) .Add("-o") .Add(Output1.AbsolutePath) .Add("-O") .Add(Output2.AbsolutePath)); await foreach (var cmdEvent in command.ListenAsync()) { switch (cmdEvent) { case StandardOutputCommandEvent e: // ? break; case StandardErrorCommandEvent e: //Console.WriteLine(e.Text); break; } } return(ExecutionResult.Next()); }
public override async Task <ExecutionResult> RunAsync(IStepExecutionContext context) { var ouput = Session.CreateFolder(); ReadAlignment = ouput.GetFile("snps.bam"); var command = Cli .Wrap("snippy") .WithArguments(args => args .Add("--force") .Add("--cpus") .Add(Environment.ProcessorCount) .Add("--outdir") .Add(ouput.AbsolutePath) .Add("--ref") .Add(Reference.AbsolutePath) .Add("--R1") .Add(Fastq1.AbsolutePath) .Add("--R2") .Add(Fastq2.AbsolutePath)); await foreach (var cmdEvent in command.ListenAsync()) { switch (cmdEvent) { case StandardOutputCommandEvent e: // ? break; case StandardErrorCommandEvent e: //Console.WriteLine(e.Text); break; } } return(ExecutionResult.Next()); }