Fix regex pattern in preprocess_collect_config

gaps/cli/preprocessing.py

@@ -150,13 +150,16 @@ def preprocess_collect_config(
     files = collect_pattern
     if files == "PIPELINE":
         files = parse_previous_status(project_dir, command_name)
-        files = [re.sub(f"{TAG}\\d+", "*", fname) for fname in files]
+        files = [re.sub(f"{TAG}\\d+", f"{TAG}*", fname) for fname in files]
 
     if isinstance(files, str):
         files = [files]
 
     if isinstance(files, abc.Sequence):
-        files = {pattern.replace("*", ""): pattern for pattern in files}
+        files = {
+            pattern.replace(f"{TAG}*", "").replace("*", ""): pattern
+            for pattern in files
+        }
 
     files = [
         (

tests/cli/test_cli.py

@@ -370,7 +370,7 @@ def test_cli_monitor(
         assert "collect-run_collect_pattern" in collected_outputs.attrs
         assert (
             Path(collected_outputs.attrs["collect-run_collect_pattern"])
-            == tmp_cwd / file_pattern
+            == tmp_cwd / file_pattern.replace("*", f"{TAG}*")
         )
 
     profiles = manual_collect(data_dir / file_pattern, "cf_profile")
@@ -487,7 +487,7 @@ def test_cli_background(
         assert "collect-run_collect_pattern" in collected_outputs.attrs
         assert (
             Path(collected_outputs.attrs["collect-run_collect_pattern"])
-            == tmp_cwd / file_pattern
+            == tmp_cwd / file_pattern.replace("*", f"{TAG}*")
         )
 
     profiles = manual_collect(data_dir / file_pattern, "cf_profile")

tests/cli/test_cli_preprocesing.py

@@ -6,6 +6,7 @@
 """
 
 import json
+import glob
 from pathlib import Path
 
 import pytest
@@ -16,6 +17,7 @@
     preprocess_collect_config,
     split_project_points_into_ranges,
 )
+from gaps.cli.config import TAG
 from gaps.exceptions import gapsConfigError
 from gaps.warn import gapsWarning
 
@@ -111,7 +113,38 @@ def test_preprocess_collect_config_pipeline_input(tmp_path):
     assert len(config["_pattern"]) == 2
     for out_fp, pattern in zip(config["_out_path"], config["_pattern"]):
         assert any(name in out_fp for name in allowed_out_fn)
-        assert out_fp == pattern.replace("*", "")
+        assert out_fp == pattern.replace(f"{TAG}*", "")
+
+
+def test_preprocess_collect_config_pipeline_input_ignores_untagged_file(
+    tmp_path,
+):
+    """Test that PIPELINE collection patterns do not match untagged files."""
+    config_fp = tmp_path / "pipe_config.json"
+    with open(config_fp, "w") as file_:
+        json.dump(SAMPLE_CONFIG, file_)
+
+    (tmp_path / "config.json").touch()
+    (tmp_path / "collect_config.json").touch()
+
+    Pipeline(config_fp)
+
+    job_file = tmp_path / "output_file_j0.h5"
+    job_file.touch()
+    (tmp_path / "output_file.h5").touch()
+    Status.make_single_job_file(
+        tmp_path,
+        pipeline_step="run",
+        job_name="test_0",
+        attrs={StatusField.OUT_FILE: job_file.as_posix()},
+    )
+
+    config = preprocess_collect_config({}, tmp_path, "collect-run")
+
+    matched_files = sorted(
+        Path(path) for path in glob.glob(config["_pattern"][0])
+    )
+    assert matched_files == [job_file]
 
 
 def test_split_project_points_into_ranges():