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| author | Justin Bedo <cu@cua0.org> | 2024-11-12 15:50:42 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2024-11-12 15:50:42 +1100 |
| commit | 58fa67ffd09d3bdfe72bef7c873ef94190dc6708 (patch) | |
| tree | 9e382c5b1da76540d6b1ca2d9a053f52042e3579 /examples/call.nix | |
| parent | 00d758934e7d5827e01585887a36913a326535ea (diff) | |
Diffstat (limited to 'examples/call.nix')
| -rw-r--r-- | examples/call.nix | 8 |
1 files changed, 4 insertions, 4 deletions
diff --git a/examples/call.nix b/examples/call.nix index 81a112e..7525835 100644 --- a/examples/call.nix +++ b/examples/call.nix @@ -1,7 +1,7 @@ # This is an example pipeline specification to do multi-sample variant calling -# with the Platypus variant caller. Each input is preprocessed by aligning +# with the Octopus 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. +# marking duplicates. Finally octopus is called over all samples. { bionix ? import <bionix> { } , inputs , ref ? bionix.ref.grch38.seq @@ -12,7 +12,7 @@ with lib; let preprocess = flip pipe [ - (bwa.align { inherit ref; }) + (bwa.align { inherit ref; RG = {SM = "sample"; ID = "sample";};}) (samtools.sort { nameSort = true; }) (samtools.fixmate { }) (samtools.sort { }) @@ -20,4 +20,4 @@ let ]; in -platypus.call { } (map preprocess inputs) +octopus.call { } (map preprocess inputs) |