3 files changed, 41 insertions, 0 deletions
diff --git a/default.nix b/default.nix
index 450118d..54d0215 100644
--- a/default.nix
+++ b/default.nix
@@ -27,6 +27,7 @@ let
     mosdepth = callBionix ./tools/mosdepth.nix {};
     mutect = callBionix ./tools/mutect.nix {};
     minimap2 = callBionix ./tools/minimap2.nix {};
+    picard = callBionix ./tools/picard.nix {};
     platypus = callBionix ./tools/platypus.nix {};
     ref = callBionix ./lib/references.nix {};
     samtools = callBionix ./tools/samtools.nix {};
diff --git a/tools/picard-markDuplicates.nix b/tools/picard-markDuplicates.nix
new file mode 100644
index 0000000..957a05e
--- /dev/null
+++ b/tools/picard-markDuplicates.nix
@@ -0,0 +1,33 @@
+{ bionix
+, flags ? null
+} :
+
+inputBam :
+
+with bionix;
+with lib;
+with types;
+
+assert (matchFiletype "picard-markDuplicates" { bam = _: true; } inputBam);
+assert (matchFileSorting
+    "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;
+}
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