nf-core · JulianFlesch · Oct 8, 2025 · Sep 9, 2025 · Sep 9, 2025 · Sep 9, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -60,6 +60,7 @@
 - Fix backwards compatibility with python 3.9 in use of Enum ([#3736](https://github.com/nf-core/tools/pull/3736))
 - Fix downloads: temporary files not moved and cleaned up correctly after singularity pull ([#3749](https://github.com/nf-core/tools/pull/3749))
 - impr devcontainer: Add hostRequirements to run with 4CPUs and 16GB ram by default ([#3746](https://github.com/nf-core/tools/pull/3746))
+- Fix Issues/3729: Remove temporary folders created from nextflow inspect during downloads ([#3750](https://github.com/nf-core/tools/pull/3750))
 - Fix diff printing to terminal ([#3759](https://github.com/nf-core/tools/pull/3759))
 - Add .nf-test/ to prettier ignore list ([#3776](https://github.com/nf-core/tools/pull/3776))
 - Update dependency prompt_toolkit to <=3.0.52 ([#3783](https://github.com/nf-core/tools/pull/3783))

diff --git a/nf_core/pipelines/download/download.py b/nf_core/pipelines/download/download.py
@@ -22,7 +22,7 @@
 from nf_core.pipelines.download.container_fetcher import ContainerFetcher
 from nf_core.pipelines.download.docker import DockerFetcher
 from nf_core.pipelines.download.singularity import SINGULARITY_CACHE_DIR_ENV_VAR, SingularityFetcher
-from nf_core.pipelines.download.utils import DownloadError
+from nf_core.pipelines.download.utils import DownloadError, intermediate_dir_with_cd
 from nf_core.pipelines.download.workflow_repo import WorkflowRepo
 from nf_core.utils import (
     NF_INSPECT_MIN_NF_VERSION,
@@ -650,19 +650,21 @@ def find_container_images(
                 profile_str += ",test,test_full"
             profile = f"-profile {profile_str}" if self.container_system else ""
 
-            # Run nextflow inspect
-            executable = "nextflow"
-            cmd_params = f"inspect -format json {profile} {workflow_directory / entrypoint}"
-            cmd_out = run_cmd(executable, cmd_params)
-            if cmd_out is None:
-                raise DownloadError("Failed to run `nextflow inspect`. Please check your Nextflow installation.")
-
-            out, _ = cmd_out
-            out_json = json.loads(out)
-            # NOTE: Should we save the container name too to have more meta information?
-            named_containers = {proc["name"]: proc["container"] for proc in out_json["processes"]}
-            # We only want to process unique containers
-            self.containers = list(set(named_containers.values()))
+            working_dir = Path().absolute()
+            with intermediate_dir_with_cd(working_dir):
+                # Run nextflow inspect
+                executable = "nextflow"
+                cmd_params = f"inspect -format json {profile} {working_dir / workflow_directory / entrypoint}"
+                cmd_out = run_cmd(executable, cmd_params)
+                if cmd_out is None:
+                    raise DownloadError("Failed to run `nextflow inspect`. Please check your Nextflow installation.")
+
+                out, _ = cmd_out
+                out_json = json.loads(out)
+                # NOTE: Should we save the container name too to have more meta information?
+                named_containers = {proc["name"]: proc["container"] for proc in out_json["processes"]}
+                # We only want to process unique containers
+                self.containers = list(set(named_containers.values()))
 
         except RuntimeError as e:
             log.error("Running 'nextflow inspect' failed with the following error")

diff --git a/nf_core/pipelines/download/utils.py b/nf_core/pipelines/download/utils.py
@@ -1,6 +1,7 @@
 import contextlib
 import importlib.resources
 import logging
+import os
 import shutil
 import tempfile
 from collections.abc import Generator
@@ -81,3 +82,21 @@ def intermediate_file_no_creation(output_path: Path) -> Generator[Path, None, No
     except:
         tmp.cleanup()
         raise
+
+
+@contextlib.contextmanager
+def intermediate_dir_with_cd(original_dir: Path, base_dir: Path = Path(".")):
+    """
+    Context manager to provide and change into a tempdir and ensure its removal and return to the
+    original_dir upon exceptions.
+    """
+
+    if not original_dir.is_dir():
+        raise DownloadError(f"Unable to setup temporary dir, original_dir does not exist: {original_dir}")
+
+    tmp = tempfile.TemporaryDirectory(dir=base_dir)
+    try:
+        os.chdir(tmp.name)
+        yield tmp
+    finally:
+        os.chdir(original_dir)