diff options
Diffstat (limited to 'examples/call.nix')
| -rw-r--r-- | examples/call.nix | 16 |
1 files changed, 9 insertions, 7 deletions
diff --git a/examples/call.nix b/examples/call.nix index 8a38fdb..81a112e 100644 --- a/examples/call.nix +++ b/examples/call.nix @@ -2,9 +2,10 @@ # 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> {} -,inputs -,ref ? bionix.ref.grch38.seq }: +{ bionix ? import <bionix> { } +, inputs +, ref ? bionix.ref.grch38.seq +}: with bionix; with lib; @@ -13,9 +14,10 @@ let preprocess = flip pipe [ (bwa.align { inherit ref; }) (samtools.sort { nameSort = true; }) - (samtools.fixmate {}) - (samtools.sort {}) - (samtools.markdup {}) + (samtools.fixmate { }) + (samtools.sort { }) + (samtools.markdup { }) ]; -in platypus.call {} (map preprocess inputs) +in +platypus.call { } (map preprocess inputs) |