nf-core · mashehu · Mar 25, 2026 · Mar 20, 2026 · Mar 20, 2026 · Mar 20, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -49,6 +49,7 @@
 - fix incorrect unqoting of `val()` version numbers ([#4042](https://github.com/nf-core/tools/pull/4042))
 - allow versions.yml in the version topics ([#4094](https://github.com/nf-core/tools/pull/4094))
 - Ensure release linting happens on branch named main ([#4121](https://github.com/nf-core/tools/pull/4121))
+- Add linting for meta and ext keys ([#4127](https://github.com/nf-core/tools/pull/4127))
 - Add strict syntax linting to template with pre-commit ([#4128](https://github.com/nf-core/tools/pull/4128))
 
 ### Modules

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
@@ -264,11 +264,61 @@ def check_script_section(self, lines):
     # check for prefix (only if module has a meta map as input)
     if self.has_meta:
         if re.search(r"\s*prefix\s*=\s*task.ext.prefix", script):
-            self.passed.append(("main_nf", "main_nf_meta_prefix", "'prefix' specified in script section", self.main_nf))
+            self.passed.append(
+                (
+                    "main_nf",
+                    "main_nf_meta_prefix",
+                    "'prefix' specified in script section",
+                    self.main_nf,
+                )
+            )
         else:
             self.failed.append(
-                ("main_nf", "main_nf_meta_prefix", "'prefix' unspecified in script section", self.main_nf)
+                (
+                    "main_nf",
+                    "main_nf_meta_prefix",
+                    "'prefix' unspecified in script section",
+                    self.main_nf,
+                )
+            )
+
+    # Validate meta keys
+    permitted_meta_keys = {"id", "single_end"}
+    invalid_meta_keys = [
+        f"{prefix}{key}"
+        for prefix, key in re.findall(r"(meta\d*\.)(\w+)\b(?!\()", script)
+        if key not in permitted_meta_keys
+    ]
+    if not invalid_meta_keys:
+        self.passed.append(("main_nf", "main_nf_meta_key", "All 'meta' keys are valid", self.main_nf))
+    else:
+        self.failed.append(
+            (
+                "main_nf",
+                "main_nf_meta_key",
+                f"Invalid 'meta' keys detected: {', '.join(invalid_meta_keys)}",
+                self.main_nf,
+            )
+        )
+
+    # Validate ext keys
+    permitted_ext_keys = {"ext.args", "ext.prefix", "ext.use_gpu"}
+    invalid_ext_keys = [
+        key
+        for key in re.findall(r"ext\.\w+", script)
+        if key not in permitted_ext_keys and not re.match(r"^ext\.args([2-9]|\d{2,})$", key)
+    ]
+    if not invalid_ext_keys:
+        self.passed.append(("main_nf", "main_nf_ext_key", "All 'ext' keys are valid", self.main_nf))
+    else:
+        self.failed.append(
+            (
+                "main_nf",
+                "main_nf_ext_key",
+                f"Invalid 'ext' keys detected: {', '.join(invalid_ext_keys)}",
+                self.main_nf,
             )
+        )
 
 
 def check_when_section(self, lines):

diff --git a/tests/modules/lint/test_lint_utils.py b/tests/modules/lint/test_lint_utils.py
@@ -13,6 +13,7 @@ def __init__(self):
         self.failed = []
 
         self.main_nf = "main_nf"
+        self.has_meta = False
 
 
 class TestModulesLint(TestModules):

diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py
@@ -2,7 +2,12 @@
 
 import nf_core.modules.lint
 from nf_core.components.nfcore_component import NFCoreComponent
-from nf_core.modules.lint.main_nf import _parse_output_topics, check_container_link_line, check_process_labels
+from nf_core.modules.lint.main_nf import (
+    _parse_output_topics,
+    check_container_link_line,
+    check_process_labels,
+    check_script_section,
+)
 
 from ...test_modules import TestModules
 from .test_lint_utils import MockModuleLint
@@ -517,3 +522,118 @@ def test_get_topics_version_yml_path_no_parens(tmp_path):
     assert any("wrong_versions_yml_emit" in str(f) for f in mock_lint_fail.failed), (
         f"Expected wrong_versions_yml_emit in failed, got: {mock_lint_fail.failed}"
     )
+
+
+def test_validate_meta_keys():
+    """Test validation of meta keys in script"""
+    mock_lint = MockModuleLint()
+
+    # Valid meta keys
+    check_script_section(
+        mock_lint,
+        [
+            """
+    def prefix = "${meta.id}"
+    def se = meta.single_end
+    def id = meta.subMap(['id'])
+    """
+        ],
+    )
+    assert len(mock_lint.failed) == 0
+
+    # Invalid meta keys
+    mock_lint.passed, mock_lint.failed = [], []
+    check_script_section(
+        mock_lint,
+        [
+            """
+    def sample = meta.sample
+    def strand = meta.strandedness
+    """
+        ],
+    )
+    assert len(mock_lint.failed) == 1
+    assert "meta.sample" in mock_lint.failed[0][2]
+    assert "meta.strandedness" in mock_lint.failed[0][2]
+
+    # meta2/meta3 with valid keys
+    mock_lint.passed, mock_lint.failed = [], []
+    check_script_section(
+        mock_lint,
+        [
+            """
+    def id1 = meta.id
+    def id2 = meta2.id
+    def se = meta3.single_end
+    """
+        ],
+    )
+    assert len(mock_lint.failed) == 0
+
+    # Mix of valid and invalid
+    mock_lint.passed, mock_lint.failed = [], []
+    check_script_section(
+        mock_lint,
+        [
+            """
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def sample = meta.sample
+    def single_end = meta.single_end
+    def custom = meta2.custom_field
+    """
+        ],
+    )
+    assert len(mock_lint.failed) == 1
+    assert "meta.sample" in mock_lint.failed[0][2]
+    assert "meta2.custom_field" in mock_lint.failed[0][2]
+
+
+def test_validate_ext_keys():
+    """Test validation of ext keys in script"""
+    mock_lint = MockModuleLint()
+
+    # Valid ext keys
+    check_script_section(
+        mock_lint,
+        [
+            """
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def use_gpu = task.ext.use_gpu ? '--gpu' : ''
+    """
+        ],
+    )
+    assert len(mock_lint.failed) == 0
+
+    # Invalid ext keys
+    mock_lint.passed, mock_lint.failed = [], []
+    check_script_section(
+        mock_lint,
+        [
+            """
+    def args1 = task.ext.args1 ?: ''
+    def custom = task.ext.custom ?: ''
+    def suffix = task.ext.suffix ?: '.bam'
+    """
+        ],
+    )
+    assert len(mock_lint.failed) == 1
+    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]
+
+    # ext.argsN where N >= 2 should be valid
+    mock_lint.passed, mock_lint.failed = [], []
+    check_script_section(
+        mock_lint,
+        [
+            """
+    def args2 = task.ext.args2 ?: ''
+    def args10 = task.ext.args10 ?: ''
+    def args99 = task.ext.args99 ?: ''
+    """
+        ],
+    )
+    assert len(mock_lint.failed) == 0