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| author | Justin Bedo <cu@cua0.org> | 2019-07-26 09:02:16 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-07-26 09:07:25 +1000 |
| commit | de8aba779f1e255838a6d583e5b311ab182ac910 (patch) | |
| tree | 6d9cfd1a12ee68c282c12958046695a5b2f83619 /examples | |
| parent | ac299f45add87dd7158776f8f8baf4139a30566a (diff) | |
Simplify example
Diffstat (limited to 'examples')
| -rw-r--r-- | examples/call.nix | 4 |
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 {}) |