import_run update

src/pipes/somatic_slurm.rs

@@ -262,6 +262,8 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
     }
 
     let mut tmp_split_dir: Option<PathBuf> = None;
+    let mut _temp_guards: Vec<TempDirGuard> = Vec::new();
+
 
     if !pod5s_to_basecall.is_empty() {
         info!(
@@ -271,7 +273,8 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
 
         // Create temporary directory containing only the POD5s that need basecalling
         let local_pod5_dir = tmp_dir.join(format!("pod5s_{}", Uuid::new_v4()));
-        let _pod5_guard = TempDirGuard::new(local_pod5_dir.clone());
+        _temp_guards.push(TempDirGuard::new(local_pod5_dir.clone()));
+
         fs::create_dir_all(&local_pod5_dir).context(format!(
             "Failed to create temporary POD5 directory: {}",
             local_pod5_dir.display()
@@ -283,13 +286,13 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
                 .file_name()
                 .ok_or_else(|| anyhow::anyhow!("Invalid POD5 filename: {}", src.display()))?;
             let dst = local_pod5_dir.join(file_name);
-            std::os::unix::fs::symlink(src, &dst).with_context(|| {
-                format!(
-                    "Failed to symlink POD5 '{}' to '{}'",
-                    src.display(),
-                    dst.display()
-                )
-            })?;
+            #[cfg(unix)]
+            std::os::unix::fs::symlink(src, &dst)
+                .with_context(|| format!("Failed to symlink {} → {}", src.display(), dst.display()))?;
+
+            #[cfg(not(unix))]
+            fs::copy(src, &dst)
+                .with_context(|| format!("Failed to copy {} → {}", src.display(), dst.display()))?;
         }
 
         let tmp_basecalled_bam = tmp_dir.join(format!("{}.bam", Uuid::new_v4()));
@@ -576,7 +579,6 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
             SlurmRunner::run(&mut index_cmd)?;
 
             // Merge into existing final BAM.
-            // SamtoolsMerge::clean_up() will remove the source BAM.
             let mut merge_cmd =
                 SamtoolsMerge::from_config(config, &case_merged_bam, &final_bam_path);
             SlurmRunner::run(&mut merge_cmd)?;
@@ -589,14 +591,6 @@ pub fn import_run(run: &Pod5sRun, config: &Config) -> anyhow::Result<()> {
 
             // First per-case BAM becomes the base final BAM.
             fs::rename(&case_merged_bam, &final_bam_path)?;
-
-            // Index the new final BAM.
-            let mut index_cmd = SamtoolsIndex {
-                bin: config.align.samtools_bin.clone(),
-                threads: config.align.samtools_view_threads,
-                bam: final_bam_path.to_string_lossy().to_string(),
-            };
-            SlurmRunner::run(&mut index_cmd)?;
         }
 
         // -----------------------------------------------------------------