tweak CLI handling to show errors

michaeljon · May 24, 2022 · f2f7e90 · f2f7e90
1 parent 8ab1a9b
commit f2f7e90
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Showing 2 changed files with 14 additions and 3 deletions.
diff --git a/Program.cs b/Program.cs
@@ -3,6 +3,7 @@
 using System.IO;
 using System.Text.Json;
 using CommandLine;
+using CommandLine.Text;
 using Ovation.FasterQC.Net.Modules;
 using Ovation.FasterQC.Net.Readers;
 using Ovation.FasterQC.Net.Utils;
@@ -31,12 +32,22 @@ private static void Main(string[] args)
                 }
             );
 
-            _ = parser.ParseArguments<CliOptions>(args)
+            var parserResult = parser.ParseArguments<CliOptions>(args);
+            parserResult
                 .WithParsed(o =>
                     {
                         Settings = o;
                         new Program().Run();
-                    });
+                    })
+                .WithNotParsed(x =>
+                {
+                    var helpText = HelpText.AutoBuild(parserResult, h =>
+                    {
+                        h.AutoVersion = false;  // hides --version
+                        return HelpText.DefaultParsingErrorsHandler(parserResult, h);
+                    }, e => e);
+                    Console.Error.WriteLine(helpText);
+                });
         }
 
         private void Run()

diff --git a/Utils/CliOptions.cs b/Utils/CliOptions.cs
@@ -24,7 +24,7 @@ public class CliOptions
         [Option('f', "format", Required = true, HelpText = "Type of input file.")]
         public ReaderType Format { get; set; }
 
-        [Option('m', "modules", Required = false, HelpText = "Space-separated list of modules to run, or 'all'.")]
+        [Option('m', "modules", Required = false, Default = new string[] { "all" }, HelpText = "Space-separated list of modules to run, or 'all'.")]
         public IEnumerable<string> ModuleNames { get; set; } = Array.Empty<string>();
 
         [Option('l', "read-limit", Required = false, HelpText = "Limit the number of reads processed")]