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-rw-r--r--examples/call.nix4
1 files changed, 2 insertions, 2 deletions
diff --git a/examples/call.nix b/examples/call.nix
index 212f430..0e4ea05 100644
--- a/examples/call.nix
+++ b/examples/call.nix
@@ -4,13 +4,13 @@
# marking duplicates. Finally platypus is called over all samples.
{bionix ? import ./.. {}
,inputs
-,ref ? null}:
+,ref ? bionix.ref.grch38.seq }:
with bionix;
let
preprocess = pipe [
- (bwa.align {ref = if ref == null then bionix.ref.grch38.seq else ref;})
+ (bwa.align { inherit ref; })
(samtools.fixmate {})
(samtools.sort {})
(samtools.markdup {})