diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index 550d0d4a9accc206fc9214d7b3baaa9101024ab9..0000000000000000000000000000000000000000
--- a/.gitmodules
+++ /dev/null
@@ -1,4 +0,0 @@
-[submodule "workflow/external_repo/astrocyte-atac-runner"]
-	path = workflow/external_repo/astrocyte-atac-runner
-	url = https://git.biohpc.swmed.edu/s219741/astrocyte-atac-runner.git
-	branch = master
diff --git a/workflow/.gitkeep b/workflow/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/workflow/external_repo/.gitkeep b/workflow/external_repo/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/workflow/external_repo/astrocyte-atac-runner/.gitkeep b/workflow/external_repo/astrocyte-atac-runner/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/workflow/file.txt b/workflow/file.txt
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000