diff --git a/.gitmodules b/.gitmodules
index 54cf7dc..ff27b7a 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -6,7 +6,3 @@
 	path = tasks
 	url = https://github.com/biowdl/tasks.git
 	branch = develop
-[submodule "scripts"]
-	path = scripts
-	url = https://github.com/biowdl/scripts.git
-	branch = develop
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5acc360..958cb5e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ that users understand how the changes affect the new version.
 
 v2.0.0-dev
 ---------------------------
++ Move pipeline out of BioWDL.
 + Make g.vcf output optional, because generating a g.vcf with DeepVariant is
 extremely slow. This changes the default behaviour.
 
diff --git a/scripts b/scripts
deleted file mode 160000
index 325a129..0000000
--- a/scripts
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 325a129c14de56b2055ee0e9e0da7dc74df5fec4