From 70ae961aba619c2cde4151772e31a079dde70226 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund@nf-co.re>
Date: Mon, 6 Jul 2026 22:51:31 -0500
Subject: [PATCH] feat(modules): flag legacy versions emits

---
 nf_core/modules/lint/main_nf.py               | 18 ++++++++++++++++-
 .../rules/main_nf_legacy_versions_emit.yml    | 17 ++++++++++++++++
 tests/modules/lint/test_main_nf.py            | 20 +++++++++++++++++++
 3 files changed, 54 insertions(+), 1 deletion(-)
 create mode 100644 nf_core/modules/lint/rules/main_nf_legacy_versions_emit.yml

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 5caa70cfcc..5d45bf9b22 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -15,6 +15,7 @@
 
 log = logging.getLogger(__name__)
 MAIN_NF_VERSIONS_YML_TOPIC_RULE = Path(__file__).parent / "rules" / "main_nf_versions_yml_topic.yml"
+MAIN_NF_LEGACY_VERSIONS_EMIT_RULE = Path(__file__).parent / "rules" / "main_nf_legacy_versions_emit.yml"
 
 
 def main_nf(
@@ -323,7 +324,7 @@ def main_nf(
             module.passed.append(
                 ("main_nf", "main_nf_version_emit", "Module emits each software version", module.main_nf)
             )
-        elif "versions" in emits:
+        elif _has_legacy_versions_emit(lines_j, lines):
             module.warned.append(
                 (
                     "main_nf",
@@ -972,6 +973,21 @@ def _parse_output_topics(self, line: str) -> list[str]:
     return output
 
 
+def _has_legacy_versions_emit(source: str, output_lines: list[str]) -> bool:
+    rule = astgrep.load_rule(MAIN_NF_LEGACY_VERSIONS_EMIT_RULE)
+    if astgrep.nextflow_available():
+        from ast_grep_py import SgRoot
+
+        root = SgRoot(source, "nextflow").root()
+        if root.find(kind="ERROR") is None:
+            config = {key: rule[key] for key in ("rule", "constraints", "utils") if key in rule}
+            return bool(root.find_all(config=config))
+
+    return any(
+        re.search(r"emit:\s*versions\b", line) and not re.search(r"topic:\s*versions\b", line) for line in output_lines
+    )
+
+
 def _has_inline_versions_yml_topic_output(source: str, output_lines: list[str], command_lines: list[str]) -> bool:
     rule = astgrep.load_rule(MAIN_NF_VERSIONS_YML_TOPIC_RULE)
     if astgrep.nextflow_available():
diff --git a/nf_core/modules/lint/rules/main_nf_legacy_versions_emit.yml b/nf_core/modules/lint/rules/main_nf_legacy_versions_emit.yml
new file mode 100644
index 0000000000..964ad2dbfa
--- /dev/null
+++ b/nf_core/modules/lint/rules/main_nf_legacy_versions_emit.yml
@@ -0,0 +1,17 @@
+# ast-grep lint rule (https://ast-grep.github.io/guide/project/lint-rule.html)
+id: main_nf_legacy_versions_emit
+language: nextflow
+severity: warning
+message: "legacy `versions` output emit"
+note: |
+  Legacy `emit: versions` outputs should migrate to version tuple outputs with
+  `topic: versions`. Template-backed modules that also set `topic: versions`
+  are intentionally allowed.
+metadata:
+  fallback-regex: a^
+rule:
+  kind: output_declaration
+  all:
+    - regex: 'emit:\s*versions\b'
+    - not:
+        regex: 'topic:\s*versions\b'
diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py
index 04a6e4e981..05aa91eeb3 100644
--- a/tests/modules/lint/test_main_nf.py
+++ b/tests/modules/lint/test_main_nf.py
@@ -8,6 +8,7 @@
 from nf_core.components.nfcore_component import NFCoreComponent
 from nf_core.modules.lint.main_nf import (
     _has_inline_versions_yml_topic_output,
+    _has_legacy_versions_emit,
     _parse_output_topics,
     check_container_link_line,
     check_nf_module_name,
@@ -43,6 +44,25 @@ def test_inline_versions_yml_topic_output_matches_full_source_with_astgrep():
     assert _has_inline_versions_yml_topic_output(source, [], [])
 
 
+@pytest.mark.skipif(not astgrep.nextflow_available(), reason="tree-sitter-nextflow parser not available")
+@pytest.mark.parametrize(
+    "output_line, expected",
+    [
+        ('path "versions.yml", emit: versions', True),
+        ('path "versions.yml", emit: versions, topic: versions', False),
+    ],
+)
+def test_legacy_versions_emit_astgrep_detection(output_line, expected):
+    source = f"""
+process TEST {{
+    output:
+    {output_line}
+}}
+"""
+
+    assert _has_legacy_versions_emit(source, []) is expected
+
+
 @pytest.mark.parametrize(
     "content,passed,warned,failed",
     [