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author | Justin Bedo <cu@cua0.org> | 2018-12-19 16:46:19 +1100 |
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committer | Justin Bedo <cu@cua0.org> | 2018-12-19 16:46:19 +1100 |
commit | 5e508d19fb2927574229df09b64c3fbfc2b752eb (patch) | |
tree | 6af14e192521cb3cd127d51dc1f502d3700d241d /example/call.nix | |
parent | a458b2813b2b0749e801098fe8aa03d8444141a6 (diff) |
examples: added example tumour-normal calling pipeline script
Diffstat (limited to 'example/call.nix')
-rw-r--r-- | example/call.nix | 19 |
1 files changed, 0 insertions, 19 deletions
diff --git a/example/call.nix b/example/call.nix deleted file mode 100644 index c9be673..0000000 --- a/example/call.nix +++ /dev/null @@ -1,19 +0,0 @@ -# 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) |