diff options
| -rw-r--r-- | tools/samtools-merge.nix | 28 | ||||
| -rw-r--r-- | tools/samtools.nix | 1 |
2 files changed, 29 insertions, 0 deletions
diff --git a/tools/samtools-merge.nix b/tools/samtools-merge.nix new file mode 100644 index 0000000..6d072b0 --- /dev/null +++ b/tools/samtools-merge.nix @@ -0,0 +1,28 @@ +{ bionix +, nixpkgs +, flags ? null +, outfmt ? null +}: + +inputs: + +with nixpkgs; +with lib; + +let + inherit (bionix.types) matchFiletype option-sort; + inputIsSorted = input: matchFiletype "samtools-merge" { + bam = _: true; #{sorting, ...}: sorting == option-sort.some (bionix.types.sorting.coord {}); + } input; +in + +assert (all inputIsSorted inputs); + +stdenv.mkDerivation { + name = "samtools-merge"; + buildInputs = [ samtools ]; + buildCommand = '' + samtools merge ${optionalString (flags != null) flags} $out ${concatStringsSep " " inputs} + ''; + passthru.filetype = (builtins.elemAt inputs 0).filetype; +} diff --git a/tools/samtools.nix b/tools/samtools.nix index 89a96b0..a05f53a 100644 --- a/tools/samtools.nix +++ b/tools/samtools.nix @@ -8,4 +8,5 @@ with bionix; flagstat = callBionix ./samtools-flagstat.nix; index = callBionix ./samtools-index.nix; sort = callBionix ./samtools-sort.nix; + merge = callBionix ./samtools-merge.nix; } |