diff options
Diffstat (limited to 'tools/picard-markDuplicates.nix')
-rw-r--r-- | tools/picard-markDuplicates.nix | 34 |
1 files changed, 17 insertions, 17 deletions
diff --git a/tools/picard-markDuplicates.nix b/tools/picard-markDuplicates.nix index 957a05e..e4b6369 100644 --- a/tools/picard-markDuplicates.nix +++ b/tools/picard-markDuplicates.nix @@ -1,8 +1,8 @@ { bionix , flags ? null -} : +}: -inputBam : +inputBam: with bionix; with lib; @@ -10,24 +10,24 @@ with types; assert (matchFiletype "picard-markDuplicates" { bam = _: true; } inputBam); assert (matchFileSorting - "picard-markDuplicates" - { coord = _: true; name = _: true; } - inputBam); + "picard-markDuplicates" + { coord = _: true; name = _: true; } + inputBam); # Note that picard markDuplicates has different behaviour depending on whether the input # is name-sorted or coordinate-sorted. stage { - name = "picard-markDuplicates"; - buildInputs = with pkgs; - [ picard-tools ]; - outputs = [ "out" "metrics" ]; - buildCommand = '' - picard MarkDuplicates \ - I=${inputBam} \ - O=$out \ - M=$metrics \ - ${optionalString (flags != null) flags} - ''; - passthru.filetype = inputBam.filetype; + name = "picard-markDuplicates"; + buildInputs = with pkgs; + [ picard-tools ]; + outputs = [ "out" "metrics" ]; + buildCommand = '' + picard MarkDuplicates \ + I=${inputBam} \ + O=$out \ + M=$metrics \ + ${optionalString (flags != null) flags} + ''; + passthru.filetype = inputBam.filetype; } |