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author | Justin Bedo <cu@cua0.org> | 2018-11-27 12:50:46 +1100 |
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committer | Justin Bedo <cu@cua0.org> | 2018-11-27 12:51:19 +1100 |
commit | fce03fcbdbea445bc058348db30ccb99274d3f96 (patch) | |
tree | 7ce6e6a0f674e0655fe210b85596670e01d76a43 /example/call.nix | |
parent | 342df165afb5961557d61bb4cb9a39b88b22d220 (diff) |
Expand README and add simple example pipeline
Diffstat (limited to 'example/call.nix')
-rw-r--r-- | example/call.nix | 19 |
1 files changed, 19 insertions, 0 deletions
diff --git a/example/call.nix b/example/call.nix new file mode 100644 index 0000000..c9be673 --- /dev/null +++ b/example/call.nix @@ -0,0 +1,19 @@ +# This is an example pipeline specification to do multi-sample variant calling +# with the Platypus variant caller. Each input is preprocessed by aligning +# against a reference genome (defaults to GRCH38), fixing mate information, and +# marking duplicates. Finally platypus is called over all samples. +{bionix ? import <bionix> {} +,nixpkgs ? import <nixpkgs> {} +,inputs +,ref ? null}: + +with bionix; + +let + preprocess = f: + samtools.markdup {} + (samtools.sort {} + (samtools.fixmate {} + (bwa.align {ref = if ref == null then bionix.ref.grch38.seq else ref;} f))); + + in platypus.call {} (map preprocess inputs) |