diff options
author | l-d-s <l@sdf.org> | 2019-05-22 09:28:58 +1000 |
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committer | l-d-s <l@sdf.org> | 2019-05-22 09:28:58 +1000 |
commit | 1d83daa0794463ecfea4ea56fe6ef917fffcd7b0 (patch) | |
tree | 92efee4155e045e5cd2132b5c9bdc07b4c4601bd /tools/picard-markDuplicates.nix | |
parent | 20ea491c74e303a3fe7a690abbf8a2632a1ec8d0 (diff) |
Unested picard-markDuplicates.
Diffstat (limited to 'tools/picard-markDuplicates.nix')
-rw-r--r-- | tools/picard-markDuplicates.nix | 26 |
1 files changed, 26 insertions, 0 deletions
diff --git a/tools/picard-markDuplicates.nix b/tools/picard-markDuplicates.nix new file mode 100644 index 0000000..aff1e32 --- /dev/null +++ b/tools/picard-markDuplicates.nix @@ -0,0 +1,26 @@ +{ bionix +, flags ? null +} : + +inputBam : + +with bionix; +with lib; +with types; + +assert (matchFiletype "picard-markDuplicates" { bam = _: true; } input); +assert (matchFileSorting "picard-markDuplicates" { coord = _: true; } input); + +stage { + name = "picard-markDuplicates"; + buildInputs = with pkgs; + [ picard-tools ]; + outputs = [ "out" "metrics" ]; + buildCommand = '' + picard MarkDuplicates \ + I=${inputBam} \ + O=$out \ + M=$metrics \ + ${optionalString (flags != null) flags} + ''; +}
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