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

@@ -1025,6 +1025,7 @@ def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix2 = task.ext.prefix2 ?: ''
     def use_gpu = task.ext.use_gpu ? '--gpu' : ''
     """
         ],
@@ -1047,6 +1048,9 @@ def suffix = task.ext.suffix ?: '.bam'
     assert "ext.args1" in mock_lint.failed[0][2]
     assert "ext.custom" in mock_lint.failed[0][2]
     assert "ext.suffix" in mock_lint.failed[0][2]
+    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]
 
     # ext.argsN where N >= 2 should be valid
     mock_lint.passed, mock_lint.failed = [], []