2 files changed, 8 insertions, 0 deletions
diff --git a/tools/octopus-call.nix b/tools/octopus-call.nix
index 252e210..8a78f01 100644
--- a/tools/octopus-call.nix
+++ b/tools/octopus-call.nix
@@ -63,7 +63,11 @@ stage {
       ${optionalString (max-genotypes != null) "--max-genotypes ${toString max-genotypes}"} \
       ${optionalString (targets != null) (handleTarget targets)} \
       ${flags}
+
+    # Strip out octopus ARGV
+    sed -i '/^##octopus=/d' $out
   '';
   passthru.filetype = filetype.vcf { inherit ref; };
   passthru.multicore = true;
+  stripStorePaths = false;
 }
diff --git a/tools/octopus-callSomatic.nix b/tools/octopus-callSomatic.nix
index f2e264c..b6106a7 100644
--- a/tools/octopus-callSomatic.nix
+++ b/tools/octopus-callSomatic.nix
@@ -77,7 +77,11 @@ stage {
       ${optionalString (targets != null) (handleTarget targets)} \
       -N $normal \
       ${flags}
+
+    # Strip out octopus ARGV
+    sed -i '/^##octopus=/d' $out
   '';
   passthru.filetype = filetype.vcf { inherit ref; };
   passthru.multicore = true;
+  stripStorePaths = false;
 }