feat: add Kraken2 report option with aggregate counts/clade

README.md

@@ -199,6 +199,12 @@ or write the kraken2 read classification output to a file
 $ nohuman -k kraken.out in.fq
 ```
 
+or write the kraken2 [sample report](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#sample-report-output-format) to file
+
+```
+$ nohuman -r kraken.report 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. 
@@ -229,6 +235,7 @@ Options:
   -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  
+  -r, --kraken-report <FILE>  Write the Kraken2 report with aggregate counts/clade to file    
   -v, --verbose               Set the logging level to verbose
   -h, --help                  Print help (see more with '--help')
   -V, --version               Print version
@@ -297,6 +304,9 @@ Options:
 
   -k, --kraken-output <FILE>
           Write the Kraken2 read classification output to a file
+
+  -r, --kraken-report <FILE>
+          Write the Kraken2 report with aggregate counts/clade to file 
 
   -v, --verbose
           Set the logging level to verbose

src/compression.rs

@@ -83,7 +83,7 @@ impl std::fmt::Display for CompressionFormat {
             CompressionFormat::Xz => "xz",
             CompressionFormat::Zstd => "zst",
         };
-        write!(f, "{}", format)
+        write!(f, "{format}",)
     }
 }
 
@@ -228,9 +228,7 @@ where
         .compression_level(Compression::default())
         .from_writer(output);
     let bytes = io::copy(input, &mut encoder)?;
-    encoder
-        .finish()
-        .map_err(|e| io::Error::new(io::ErrorKind::Other, e))?;
+    encoder.finish().map_err(io::Error::other)?;
 
     Ok(bytes)
 }

src/download.rs

@@ -55,7 +55,7 @@ fn compute_md5(path: &Path) -> Result<String, DownloadError> {
         hasher.consume(&buffer[..n]);
     }
     let result = hasher.compute();
-    Ok(format!("{:x}", result))
+    Ok(format!("{result:x}",))
 }
 
 async fn download_from_url(url: &str, dest: &Path) -> Result<(), DownloadError> {

src/lib.rs

@@ -40,10 +40,10 @@ impl CommandRunner {
 
         let stderr_log = String::from_utf8_lossy(&output.stderr);
         if !output.status.success() {
-            return Err(io::Error::new(
-                io::ErrorKind::Other,
-                format!("{} failed with stderr {}", self.command, stderr_log),
-            ));
+            return Err(io::Error::other(format!(
+                "{} failed with stderr {}",
+                self.command, stderr_log
+            )));
         }
 
         debug!("kraken2 stderr:\n {}", stderr_log);
@@ -118,7 +118,7 @@ pub fn check_path_exists<S: AsRef<OsStr> + ?Sized>(s: &S) -> Result<PathBuf, Str
     if path.exists() {
         Ok(path)
     } else {
-        Err(format!("{:?} does not exist", path))
+        Err(format!("{path:?} does not exist",))
     }
 }
 
@@ -152,8 +152,7 @@ pub fn validate_db_directory(path: &Path) -> Result<PathBuf, String> {
     }
 
     Err(format!(
-        "Required files ({}) not found in {:?} or its 'db' subdirectory",
-        files_str, path
+        "Required files ({files_str}) not found in {path:?} or its 'db' subdirectory",
     ))
 }
 

src/main.rs

@@ -81,6 +81,10 @@ struct Args {
     #[arg(short, long, value_name = "FILE")]
     kraken_output: Option<PathBuf>,
 
+    /// Write the Kraken2 report with aggregate counts/clade to file
+    #[arg(short = 'r', long, value_name = "FILE")]
+    kraken_report: Option<PathBuf>,
+
     /// Set the logging level to verbose
     #[arg(short, long)]
     verbose: bool,
@@ -166,6 +170,11 @@ fn main() -> Result<()> {
         "--confidence",
         &confidence,
     ];
+
+    if let Some(report_path) = args.kraken_report.as_ref().and_then(|p| p.to_str()) {
+        kraken_cmd.extend(&["--report", report_path]);
+    }
+
     match input.len() {
         0 => bail!("No input files provided"),
         2 => kraken_cmd.push("--paired"),
@@ -306,6 +315,14 @@ fn main() -> Result<()> {
         }
     }
 
+    if kraken_output != "/dev/null" {
+        info!("Kraken output file written to: {:?}", &kraken_output);
+    }
+
+    if let Some(report_path) = &args.kraken_report {
+        info!("Kraken report file written to: {:?}", &report_path);
+    }
+
     // cleanup the temporary directory, but only issue a warning if it fails
     if let Err(e) = tmpdir.close() {
         warn!("Failed to remove temporary output directory: {}", e);