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-rw-r--r--tools/octopus-call.nix4
-rw-r--r--tools/octopus-callSomatic.nix4
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;
}