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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) |