https://github.com/bazelbuild/bazel/issues/6864

readme.patch

diff --git a/README.md b/README.md
index 20d88da..ffb8457 100644
--- a/README.md
+++ b/README.md
@@ -1 +1 @@
-# This is not patched
+# THIS IS PATCHED

BUILD.bazel

genrule(
    name = "readme",
    srcs = ["@com_github_ashi009_bazel_repo_rule_test//:README.md"],
    outs = ["readme"],
    cmd = "cat $(location @com_github_ashi009_bazel_repo_rule_test//:README.md) | tee $@",
)

test-patched.bzl

load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive")

def test_patched_dependency():
    http_archive(
        name = "com_github_ashi009_bazel_repo_rule_test",
        patch_args = ["-p1"],
        patches = ["//:readme.patch"],
        strip_prefix = "bazel-repo-rule-test-5689dd63c35cef83099a270970aad889f22a2909",
        type = "zip",
        urls = ["https://codeload.github.com/ashi009/bazel-repo-rule-test/zip/5689dd63c35cef83099a270970aad889f22a2909"],
    )

test.bzl

load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive")

def test_dependency():
    http_archive(
        name = "com_github_ashi009_bazel_repo_rule_test",
        strip_prefix = "bazel-repo-rule-test-5689dd63c35cef83099a270970aad889f22a2909",
        type = "zip",
        urls = ["https://codeload.github.com/ashi009/bazel-repo-rule-test/zip/5689dd63c35cef83099a270970aad889f22a2909"],
    )

WORKSPACE

load("//:test.bzl", "test_dependency", "test_patched_dependency")

test_dependency()

load("//:test-patched.bzl", "test_patched_dependency")

test_patched_dependency()

# bazel build //:readme
# # This is not patched

WORKSPACE.1

load("//:test-patched.bzl", "test_patched_dependency")

test_patched_dependency()

load("//:test.bzl", "test_dependency")

test_dependency()

# bazel build //:readme
# # THIS IS PATCHED

The repository being loaded is at https://github.com/ashi009/bazel-repo-rule-test