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authorJustin Bedo <cu@cua0.org>2019-07-26 09:02:16 +1000
committerJustin Bedo <cu@cua0.org>2019-07-26 09:07:25 +1000
commitde8aba779f1e255838a6d583e5b311ab182ac910 (patch)
tree6d9cfd1a12ee68c282c12958046695a5b2f83619
parentac299f45add87dd7158776f8f8baf4139a30566a (diff)
Simplify example
-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 {})