feat: add kraken2 classification output file option -k

README.md

@@ -193,6 +193,14 @@ Set a [minimum confidence score][conf] for kraken2 classifications
 $ nohuman --conf 0.5 in.fq
 ```
 
+or write the kraken2 read classification output to a file
+
+```
+$ nohuman -k kraken.out in.fq
+```
+
+```
+
 > [!TIP]
 > Compressed output will be inferred from the specified output path(s). If no output path is provided, the same
 > compression as the input will be used. To override the output compression format, use the `--output-type` option. 
@@ -222,6 +230,7 @@ Options:
   -t, --threads <INT>         Number of threads to use in kraken2 and optional output compression. Cannot be 0 [default: 1]
   -H, --human                 Output human reads instead of removing them
   -C, --conf <[0, 1]>         Kraken2 minimum confidence score [default: 0.0]
+  -k, --kraken-output <FILE>  Write the Kraken2 read classification output to a file  
   -v, --verbose               Set the logging level to verbose
   -h, --help                  Print help (see more with '--help')
   -V, --version               Print version
@@ -288,6 +297,9 @@ Options:
 
           [default: 0.0]
           
+  -k, --kraken-output <FILE>
+          Write the Kraken2 read classification output to a file
+
   -v, --verbose
           Set the logging level to verbose
 

src/main.rs

@@ -77,6 +77,10 @@ struct Args {
     #[arg(short = 'C', long = "conf", value_name = "[0, 1]", default_value = "0.0", value_parser = parse_confidence_score)]
     confidence: f32,
 
+    /// Write the Kraken2 read classification output to a file.
+    #[arg(short, long, value_name = "FILE")]
+    kraken_output: Option<PathBuf>,
+
     /// Set the logging level to verbose
     #[arg(short, long)]
     verbose: bool,
@@ -144,8 +148,8 @@ fn main() -> Result<()> {
     // error out if input files are not provided, otherwise unwrap to a variable
     let input = args.input.context("No input files provided")?;
 
-    let temp_kraken_output =
-        tempfile::NamedTempFile::new().context("Failed to create temporary kraken output file")?;
+    let kraken_output = args.kraken_output.unwrap_or(PathBuf::from("/dev/null"));
+    let kraken_output = kraken_output.to_string_lossy();
     let threads = args.threads.to_string();
     let confidence = args.confidence.to_string();
     let db = validate_db_directory(&args.database)
@@ -158,7 +162,7 @@ fn main() -> Result<()> {
         "--db",
         &db,
         "--output",
-        temp_kraken_output.path().to_str().unwrap(),
+        &kraken_output,
         "--confidence",
         &confidence,
     ];