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| author | l-d-s <distefano.l@wehi.edu.au> | 2019-05-30 13:14:19 +1000 |
|---|---|---|
| committer | l-d-s <distefano.l@wehi.edu.au> | 2019-05-30 13:14:19 +1000 |
| commit | ae7f055db36fda71d28e58fd22ee6ffc25e01dee (patch) | |
| tree | 03e98f7c3208f642fb325cb04503e065d623df70 /tools | |
| parent | 867e68554307d45e102ba3267f5f469d02fc6a86 (diff) | |
| parent | 1d83daa0794463ecfea4ea56fe6ef917fffcd7b0 (diff) | |
Merge branch 'add-picard' of mac2559:~/Projects/bionix
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/picard-markDuplicates.nix | 26 | ||||
| -rw-r--r-- | tools/picard.nix | 7 |
2 files changed, 33 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} + ''; +}
\ No newline at end of file diff --git a/tools/picard.nix b/tools/picard.nix new file mode 100644 index 0000000..551995f --- /dev/null +++ b/tools/picard.nix @@ -0,0 +1,7 @@ +{ bionix }: + +with bionix; + +{ + markDuplicates = callBionixE ./picard-markDuplicates.nix; +}
\ No newline at end of file |