diff --git a/bam_collapsing b/bam_collapsing
index 1b0e47a..2312972 160000
--- a/bam_collapsing
+++ b/bam_collapsing
@@ -1 +1 @@
-Subproject commit 1b0e47a8e73c3b8b2aa7178100c5d48f45749533
+Subproject commit 2312972ac9a74902c352ed235d76baab5854182c
diff --git a/command_line_tools b/command_line_tools
index 6a5bea1..1f1e961 160000
--- a/command_line_tools
+++ b/command_line_tools
@@ -1 +1 @@
-Subproject commit 6a5bea1a3aaecea03d362b71a2a88c07a9b649ef
+Subproject commit 1f1e9616a4ba12a39e2c6c08339b9a7b2d9b9ad0
diff --git a/subworkflows b/subworkflows
index 31fa336..49f07d5 160000
--- a/subworkflows
+++ b/subworkflows
@@ -1 +1 @@
-Subproject commit 31fa336f7d9bfdf2bb561d43f1f1979be83060c9
+Subproject commit 49f07d58824d9998986272890699f1df26074848
diff --git a/uncollapsed_bam_generation b/uncollapsed_bam_generation
index 32d569d..d48d039 160000
--- a/uncollapsed_bam_generation
+++ b/uncollapsed_bam_generation
@@ -1 +1 @@
-Subproject commit 32d569da66a89119c37ed7c1f0e43312e865e993
+Subproject commit d48d039aba7c8cac4fd809eb75a94ecd62d640bd