Allow task.ext.prefix2 in modules linting

CHANGELOG.md

@@ -62,6 +62,7 @@
 - fix linting with missing input ([#4202](https://github.com/nf-core/tools/pull/4202))
 - fix(lint): use correct config key zenodo_doi ([#4201](https://github.com/nf-core/tools/pull/4201))
 - add missing lint test documentation and add pre-commit check for them ([#4052](https://github.com/nf-core/tools/pull/4052))
+- Allow `prefix2` for the ext keys linting ([#4234](https://github.com/nf-core/tools/pull/4234))
 
 ### Modules
 

nf_core/modules/lint/main_nf.py

@@ -320,7 +320,7 @@ def check_script_section(self, lines):
         )
 
     # Validate ext keys
-    permitted_ext_keys = {"ext.args", "ext.prefix", "ext.use_gpu"}
+    permitted_ext_keys = {"ext.args", "ext.prefix", "ext.prefix2", "ext.use_gpu"}
     invalid_ext_keys = [
         key
         for key in re.findall(r"\bext\.\w+", script)

tests/modules/lint/test_main_nf.py

@@ -1062,6 +1062,35 @@ def args99 = task.ext.args99 ?: ''
     )
     assert len(mock_lint.failed) == 0
 
+    # ext.prefix2 should be valid, but not other numbers
+    mock_lint.passed, mock_lint.failed = [], []
+    check_script_section(
+        mock_lint,
+        [
+            """
+    def prefix2 = task.ext.prefix2 ?: ''
+    """
+        ],
+    )
+    assert len(mock_lint.failed) == 0
+
+    # ext.prefix1 or ext.prefix3+ should be invalid
+    mock_lint.passed, mock_lint.failed = [], []
+    check_script_section(
+        mock_lint,
+        [
+            """
+    def prefix1 = task.ext.prefix1 ?: ''
+    def prefix3 = task.ext.prefix3 ?: ''
+    def prefix22 = task.ext.prefix22 ?: ''
+    """
+        ],
+    )
+    assert len(mock_lint.failed) == 1
+    assert "ext.prefix1" in mock_lint.failed[0][2]
+    assert "ext.prefix3" in mock_lint.failed[0][2]
+    assert "ext.prefix22" in mock_lint.failed[0][2]
+
     # Check false positive matches, e.g. text.tokenize()
     mock_lint.passed, mock_lint.failed = [], []
     check_script_section(