拓展分析运行已发布时个别样例报前缀不对的问题

gfa_core/extension_stage_lightweight/runtime_binding.py

@@ -1333,6 +1333,15 @@ def _binding_replacements(
     }
     patched_path_roots: list[tuple[str, str]] = []
 
+    prefix = resolved.get("prefix_binding")
+    prefix_old = prefix.get("old_prefix") if isinstance(prefix, dict) else None
+    prefix_new = prefix.get("new_prefix") if isinstance(prefix, dict) else None
+    participating_inputs = (
+        set(prefix.get("participating_inputs") or ())
+        if isinstance(prefix, dict)
+        else set()
+    )
+
     def add(binding_key: str, original: str, replacement: str) -> None:
         if replacement == original:
             return
@@ -1349,14 +1358,28 @@ def _binding_replacements(
         runtime = Path(str(binding.get("runtime_path") or ""))
         binding_key = f"path:{original}"
         replacement = runtime.name
+        # When the output prefix is derived from an input name (e.g. seqkit
+        # derives ``split_fasta/Ft.SPL.pep.part_001.fasta`` from the input
+        # ``Ft.SPL.pep.fasta``), the participating input must be renamed as
+        # well. Otherwise the tool keeps writing outputs under the original
+        # prefix and the renamed outputs never materialise. ``output.fasta``
+        # is symlinked into the work tree by render_runtime_package.
+        if (
+            isinstance(prefix_old, str)
+            and isinstance(prefix_new, str)
+            and original in participating_inputs
+            and _output_has_prefix(replacement, prefix_old)
+        ):
+            replacement = _replace_output_prefix(
+                replacement, prefix_old, prefix_new
+            )
         add(binding_key, original, replacement)
         if replacement != original and binding_key in patchable:
             patched_path_roots.append((original, replacement))
 
-    prefix = resolved.get("prefix_binding")
     if isinstance(prefix, dict):
-        old_prefix = prefix.get("old_prefix")
-        new_prefix = prefix.get("new_prefix")
+        old_prefix = prefix_old
+        new_prefix = prefix_new
         if isinstance(old_prefix, str) and isinstance(new_prefix, str):
             for reference in contract.get("path_references", []):
                 if not isinstance(reference, dict):

gfa_core/extension_stage_lightweight/service.py

@@ -621,10 +621,13 @@ class LightweightExtensionService:
     def _job_path(path: Path, roots: tuple[Path, Path]) -> Path:
         candidate = Path(os.path.abspath(Path(path).expanduser())).resolve()
         resolved_roots = tuple(root.resolve() for root in roots)
-        if not candidate.is_file() or not any(
-            candidate.is_relative_to(root) for root in resolved_roots
-        ):
-            raise ValueError("runtime input must be a file inside the selected job")
+        inside = any(candidate.is_relative_to(root) for root in resolved_roots)
+        if not candidate.is_file():
+            raise ValueError(f"runtime input file not found: {candidate}")
+        if not inside:
+            raise ValueError(
+                f"runtime input must be a file inside the selected job: {candidate}"
+            )
         return candidate
 
     def _execute(