diff options
| -rw-r--r-- | tools/samtools-fixmate.nix | 25 | ||||
| -rw-r--r-- | tools/samtools.nix | 1 |
2 files changed, 26 insertions, 0 deletions
diff --git a/tools/samtools-fixmate.nix b/tools/samtools-fixmate.nix new file mode 100644 index 0000000..6cb31bb --- /dev/null +++ b/tools/samtools-fixmate.nix @@ -0,0 +1,25 @@ +{ bionix +, nixpkgs +, mateScore ? false +, flags ? null +}: + +input: + +with nixpkgs; +with lib; +with bionix.types; + +assert (matchFiletype "samtools-fixmate" { bam = _: true; } input); +assert (matchFileSorting "samtools-fixmate" { name = _: true; } input); + +stdenv.mkDerivation { + name = "samtools-fixmate"; + buildInputs = [ samtools ]; + buildCommand = '' + samtools fixmate \ + ${optionalString mateScore "-m"} \ + ${optionalString (flags != null) flags} -O bam ${input} $out + ''; + passthru.filetype = input.filetype; +} diff --git a/tools/samtools.nix b/tools/samtools.nix index ea773eb..e26d996 100644 --- a/tools/samtools.nix +++ b/tools/samtools.nix @@ -10,4 +10,5 @@ with bionix; dict = callBionix ./samtools-dict.nix; sort = callBionix ./samtools-sort.nix; merge = callBionix ./samtools-merge.nix; + fixmate = callBionix ./samtools-fixmate.nix; } |