diff options
Diffstat (limited to 'examples/call.nix')
| -rw-r--r-- | examples/call.nix | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/examples/call.nix b/examples/call.nix index 212f430..0e4ea05 100644 --- a/examples/call.nix +++ b/examples/call.nix @@ -4,13 +4,13 @@ # marking duplicates. Finally platypus is called over all samples. {bionix ? import ./.. {} ,inputs -,ref ? null}: +,ref ? bionix.ref.grch38.seq }: with bionix; let preprocess = pipe [ - (bwa.align {ref = if ref == null then bionix.ref.grch38.seq else ref;}) + (bwa.align { inherit ref; }) (samtools.fixmate {}) (samtools.sort {}) (samtools.markdup {}) |