diff options
Diffstat (limited to 'examples/call.nix')
| -rw-r--r-- | examples/call.nix | 14 |
1 files changed, 7 insertions, 7 deletions
diff --git a/examples/call.nix b/examples/call.nix index c9be673..2b63ae2 100644 --- a/examples/call.nix +++ b/examples/call.nix @@ -3,17 +3,17 @@ # 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))); + preprocess = pipe [ + (bwa.align {ref = if ref == null then bionix.ref.grch38.seq else ref;}) + (samtools.fixmate {}) + (samtools.sort {}) + (samtools.markdup {}) + ]; - in platypus.call {} (map preprocess inputs) +in platypus.call {} (map preprocess inputs) |