init: samtools-markdup

2 files changed, 23 insertions, 0 deletions

diff --git a/tools/samtools-markdup.nix b/tools/samtools-markdup.nix
new file mode 100644
index 0000000..73094f2
--- /dev/null
+++ b/tools/samtools-markdup.nix
@@ -0,0 +1,22 @@
+{ bionix
+, nixpkgs
+, flags ? null
+}:
+
+input:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+
+assert (matchFiletype "samtools-markdup" { bam = _: true; } input);
+assert (matchFileSorting "samtools-markdup" { coord = _: true; } input);
+
+stdenv.mkDerivation {
+  name = "samtools-markdup";
+  buildInputs = [ samtools ];
+  buildCommand = ''
+    samtools markdup ${optionalString (flags != null) flags} ${input} $out
+  '';
+  passthru.filetype = input.filetype;
+}
diff --git a/tools/samtools.nix b/tools/samtools.nix
index e26d996..62414df 100644
--- a/tools/samtools.nix
+++ b/tools/samtools.nix
@@ -10,5 +10,6 @@ with bionix;
   dict = callBionix ./samtools-dict.nix;
   sort = callBionix ./samtools-sort.nix;
   merge = callBionix ./samtools-merge.nix;
+  markdup = callBionix ./samtools-markdup.nix;
   fixmate = callBionix ./samtools-fixmate.nix;
 }