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());
}
