diff --git a/dvc/dependency/base.py b/dvc/dependency/base.py
--- a/dvc/dependency/base.py
+++ b/dvc/dependency/base.py
@@ -15,11 +15,19 @@ def __init__(self, path):
         super(DependencyIsNotFileOrDirError, self).__init__(msg)
 
 
+class DependencyIsStageFileError(DvcException):
+    def __init__(self, path):
+        super(DependencyIsStageFileError, self).__init__(
+            "Stage file '{}' cannot be a dependency.".format(path)
+        )
+
+
 class DependencyBase(object):
     IS_DEPENDENCY = True
 
     DoesNotExistError = DependencyDoesNotExistError
     IsNotFileOrDirError = DependencyIsNotFileOrDirError
+    IsStageFileError = DependencyIsStageFileError
 
     def update(self):
         pass
diff --git a/dvc/output/base.py b/dvc/output/base.py
--- a/dvc/output/base.py
+++ b/dvc/output/base.py
@@ -32,6 +32,13 @@ def __init__(self, path):
         super(OutputAlreadyTrackedError, self).__init__(msg)
 
 
+class OutputIsStageFileError(DvcException):
+    def __init__(self, path):
+        super(OutputIsStageFileError, self).__init__(
+            "Stage file '{}' cannot be an output.".format(path)
+        )
+
+
 class OutputBase(object):
     IS_DEPENDENCY = False
 
@@ -57,6 +64,7 @@ class OutputBase(object):
 
     DoesNotExistError = OutputDoesNotExistError
     IsNotFileOrDirError = OutputIsNotFileOrDirError
+    IsStageFileError = OutputIsStageFileError
 
     sep = "/"
 
@@ -71,6 +79,7 @@ def __init__(
         persist=False,
         tags=None,
     ):
+        self._validate_output_path(path)
         # This output (and dependency) objects have too many paths/urls
         # here is a list and comments:
         #
@@ -415,3 +424,10 @@ def get_used_cache(self, **kwargs):
         ret.extend(self._collect_used_dir_cache(**kwargs))
 
         return ret
+
+    @classmethod
+    def _validate_output_path(cls, path):
+        from dvc.stage import Stage
+
+        if Stage.is_valid_filename(path):
+            raise cls.IsStageFileError(path)

As a first step we might just add a check that dependency is not a dvc file and throw an error. Having it as a feature also sounds quite neat, so one could do `-d my.dvc` which would mean "depend on all outputs of my.dvc". Not sure if that feature is desirable though, since it might be used by accident causing some obscure bugs in the pipeline.
Discord context https://discordapp.com/channels/485586884165107732/485596304961962003/605892459461083140
ohh, @efiop, that sounds really neat! never thought about it, and it make sense since "the output of  a stage become the input of the next one".
diff --git a/tests/func/test_run.py b/tests/func/test_run.py
--- a/tests/func/test_run.py
+++ b/tests/func/test_run.py
@@ -7,8 +7,10 @@
 import filecmp
 import pytest
 
+from dvc.dependency.base import DependencyIsStageFileError
 from dvc.main import main
 from dvc.output import OutputBase
+from dvc.output.base import OutputIsStageFileError
 from dvc.repo import Repo as DvcRepo
 from dvc.utils import file_md5
 from dvc.utils.stage import load_stage_file
@@ -941,3 +943,21 @@ def test_bad_stage_fname(repo_dir, dvc_repo):
 
     # Check that command hasn't been run
     assert not os.path.exists("out")
+
+
+def test_should_raise_on_stage_dependency(repo_dir, dvc_repo):
+    with pytest.raises(DependencyIsStageFileError):
+        dvc_repo.run(
+            cmd="python {} {} {}".format(repo_dir.CODE, repo_dir.FOO, "out"),
+            deps=[repo_dir.FOO, "name.dvc"],
+            outs=["out"],
+        )
+
+
+def test_should_raise_on_stage_output(repo_dir, dvc_repo):
+    with pytest.raises(OutputIsStageFileError):
+        dvc_repo.run(
+            cmd="python {} {} {}".format(repo_dir.CODE, repo_dir.FOO, "out"),
+            deps=[repo_dir.FOO],
+            outs=["name.dvc"],
+        )
diff --git a/tests/unit/test_stage.py b/tests/unit/test_stage.py
--- a/tests/unit/test_stage.py
+++ b/tests/unit/test_stage.py
@@ -70,7 +70,7 @@ def test_stage_fname(add):
 
 
 def test_stage_update(mocker):
-    dep = DependencyREPO({"url": "example.com"}, None, None)
+    dep = DependencyREPO({"url": "example.com"}, None, "dep_path")
     mocker.patch.object(dep, "update", return_value=None)
 
     stage = Stage(None, "path", deps=[dep])

run: warning/exception when dependency is a dvc-file
It doesn't make a lot of sense to depend on a dvc-file, however, the interface is not intuitive enough to prevent this.

If we want to allow this behavior, it should be with a warning.

tests/unit/test_stage.py::test_stage_checksum tests/unit/test_stage.py::test_wdir_default_ignored tests/unit/test_stage.py::test_wdir_non_default_is_not_ignored tests/unit/test_stage.py::test_meta_ignored tests/unit/test_stage.py::TestPathConversion::test tests/unit/test_stage.py::test_stage_fname[True] tests/unit/test_stage.py::test_stage_fname[False] tests/unit/test_stage.py::test_stage_update tests/unit/test_stage.py::test_stage_run_ignore_sigint tests/unit/test_stage.py::test_always_changed