diff --git a/CHANGELOG.md b/CHANGELOG.md
index 07463f8f65..bd5a3abdee 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,15 +4,15 @@
 
 ### General
 
-- dockerhub action: add disk clean-up step and combine the two actions ([#3926](https://github.com/nf-core/tools/pull/3926))
-- Update actions/setup-python digest to 83679a8 ([#3928](https://github.com/nf-core/tools/pull/3928))
 - Switch from pre-commit to prek for pre-commit hooks in development([#3899](https://github.com/nf-core/tools/pull/3899))
+- Fix docker errors in test ([#3924](https://github.com/nf-core/tools/pull/3924))
 - switch to uv and pyproject.toml ([#3925](https://github.com/nf-core/tools/pull/3925))
+- dockerhub action: add disk clean-up step and combine the two actions ([#3926](https://github.com/nf-core/tools/pull/3926))
+- Update actions/setup-python digest to 83679a8 ([#3928](https://github.com/nf-core/tools/pull/3928))
 - Pin j178/prek-action action to 91fd7d7 ([#3931](https://github.com/nf-core/tools/pull/3931))
 - add pre-commit hook to keep uv.lock in sync ([#3933](https://github.com/nf-core/tools/pull/3933))
 - Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 2be0f5a ([#3946](https://github.com/nf-core/tools/pull/3946))
 - Fix quote handling in meta.yml ([#3948](https://github.com/nf-core/tools/pull/3948))
-- Fix docker errors in test ([#3924](https://github.com/nf-core/tools/pull/3924))
 - Update actions/checkout digest to 8e8c483 ([#3956](https://github.com/nf-core/tools/pull/3956))
 - Update GitHub Actions ([#3957](https://github.com/nf-core/tools/pull/3957))
 - Update astral-sh/setup-uv digest to ed21f2f ([#3959](https://github.com/nf-core/tools/pull/3959))
@@ -23,6 +23,7 @@
 ### Linting
 
 - fix test for linting for version.yml ([#3947](https://github.com/nf-core/tools/pull/3947))
+- Fix bugs in subworkflows lint causing false positive warnings ([#3968](https://github.com/nf-core/tools/pull/3968))
 
 ### Modules
 
diff --git a/nf_core/subworkflows/lint/main_nf.py b/nf_core/subworkflows/lint/main_nf.py
index cb2177ed5d..6c99e99606 100644
--- a/nf_core/subworkflows/lint/main_nf.py
+++ b/nf_core/subworkflows/lint/main_nf.py
@@ -51,15 +51,15 @@ def main_nf(_, subworkflow: NFCoreComponent) -> tuple[list[str], list[str]]:
     workflow_lines = []
     main_lines = []
     for line in lines:
-        if re.search(r"^\s*workflow\s*\w*\s*{", line) and state == "subworkflow":
+        if not _is_empty(line) and re.search(r"^\s*workflow\s*\w*\s*{", line) and state in ["subworkflow", "emit"]:
             state = "workflow"
-        if re.search(r"take\s*:", line) and state in ["workflow"]:
+        if not _is_empty(line) and re.search(r"take\s*:", line) and state in ["workflow"]:
             state = "take"
             continue
-        if re.search(r"main\s*:", line) and state in ["take", "workflow"]:
+        if not _is_empty(line) and re.search(r"main\s*:", line) and state in ["take", "workflow"]:
             state = "main"
             continue
-        if re.search(r"emit\s*:", line) and state in ["take", "main", "workflow"]:
+        if not _is_empty(line) and re.search(r"emit\s*:", line) and state in ["take", "main", "workflow"]:
             state = "emit"
             continue