fix(preseq): record status for unestimable libraries

docs/src/content/docs/rna/preseq.mdx

@@ -56,8 +56,23 @@ all files directly to the output directory instead.
 <FileTree>
 - preseq/
   - `sample.lc_extrap.txt` Library complexity extrapolation curve
+  - `sample.preseq_skipped.txt` Status when the estimator rejects the analysis
 </FileTree>
 
+When the estimator rejects an analysis (for example, too few distinct molecules
+or a failed Good-Toulmin check), RustQC keeps the warning and writes only
+`<sample>.preseq_skipped.txt`, with `STATUS` and `REASON` columns and one
+`skipped` row. It does not write a complexity curve or substitute numeric
+predictions. MultiQC 1.35 ignores this status file; header-only complexity
+tables can instead fail in that version's Preseq module.
+
+After a successful enabled rerun in the same output layout, only the current
+artifact remains for that sample: a skipped estimate removes the previous curve,
+and an estimated curve removes the previous skipped status. Files in another
+previously used output layout are not removed. File write or removal errors fail
+the command; old or partially updated files may remain after a failure.
+Disabling preseq creates no preseq outputs and leaves existing files untouched.
+
 ### Complexity curve
 
 **File:** `<sample>.lc_extrap.txt`

src/main.rs

@@ -1838,6 +1838,7 @@ fn write_rseqc_outputs(
         };
         std::fs::create_dir_all(&preseq_dir)?;
         let output_path = preseq_dir.join(format!("{}.lc_extrap.txt", sample_name));
+        let skipped_path = preseq_dir.join(format!("{}.preseq_skipped.txt", sample_name));
         accum.finalize();
         let total_reads = accum.total_fragments;
         let n_distinct = accum.n_distinct();
@@ -1860,13 +1861,19 @@ fn write_rseqc_outputs(
                     &output_path,
                     params.config.preseq.confidence_level,
                 )?;
+                remove_stale_preseq_output(&skipped_path)?;
                 let p = output_path.display().to_string();
                 ui.output_item("preseq", &p);
                 ui.output_detail(&format!("{} extrapolation points", result.curve.len(),));
                 written.push(("preseq".into(), p));
             }
             Err(e) => {
                 ui.warn(&format!("preseq: skipped — {}", e));
+                rna::preseq::write_skipped_output(&skipped_path, &e.to_string())?;
+                remove_stale_preseq_output(&output_path)?;
+                let p = skipped_path.display().to_string();
+                ui.output_item("preseq status", &p);
+                written.push(("preseq status".into(), p));
             }
         }
     }
@@ -1876,3 +1883,12 @@ fn write_rseqc_outputs(
         infer_experiment: infer_experiment_result,
     })
 }
+
+fn remove_stale_preseq_output(path: &Path) -> Result<()> {
+    match std::fs::remove_file(path) {
+        Ok(()) => Ok(()),
+        Err(e) if e.kind() == std::io::ErrorKind::NotFound => Ok(()),
+        Err(e) => Err(e)
+            .with_context(|| format!("Failed to remove stale preseq output: {}", path.display())),
+    }
+}

src/rna/preseq.rs

@@ -1239,6 +1239,24 @@ fn quantile(sorted: &[f64], q: f64) -> f64 {
 // Output
 // ============================================================================
 
+/// Write a skipped-status TSV when the estimator rejects an analysis, without predictions.
+pub fn write_skipped_output(output_path: &Path, reason: &str) -> Result<()> {
+    let mut f = std::fs::File::create(output_path).with_context(|| {
+        format!(
+            "Failed to create preseq skipped-status output: {}",
+            output_path.display()
+        )
+    })?;
+    let reason = reason.replace(['\t', '\r', '\n'], " ");
+    writeln!(f, "STATUS\tREASON\nskipped\t{reason}").with_context(|| {
+        format!(
+            "Failed to write preseq skipped-status output: {}",
+            output_path.display()
+        )
+    })?;
+    Ok(())
+}
+
 /// Write the preseq lc_extrap output in TSV format.
 ///
 /// Output format matches preseq's lc_extrap output: