1 files changed, 33 insertions, 18 deletions
diff --git a/tools/mosdepth-depth.nix b/tools/mosdepth-depth.nix
index 2a72989..4627071 100644
--- a/tools/mosdepth-depth.nix
+++ b/tools/mosdepth-depth.nix
@@ -1,21 +1,36 @@
-{ bionix
-, indexAttrs ? { }
-, flags ? null
+{
+  bionix,
+  indexAttrs ? {},
+  targets ? null,
+  flags ? null,
 }:
-
 with bionix;
 with lib;
-
-input:
-
-stage {
-  name = "mosdepth-depth";
-  buildInputs = with pkgs; [ mosdepth ];
-  buildCommand = ''
-    mkdir $out
-    ln -s ${input} input.bam
-    ln -s ${bionix.samtools.index indexAttrs input} input.bam.bai
-    mosdepth -t $NIX_BUILD_CORES ${optionalString (flags != null) flags} $out/out input.bam
-  '';
-  passthru.multicore = true;
-}
+  input: let
+    handleTarget = x: let
+      type = builtins.typeOf x;
+      handler = handlers."${type}" or (builtins.throw "mosdepth-depth:unhandled target type:${type}");
+      handlers = {
+        string = handleTarget [x];
+        list = let
+          file = pkgs.writeText "target.bed" (concatStringsSep "\n" x);
+        in "-b ${file}";
+        path = "-b ${x}";
+        set = "-b ${x}";
+      };
+    in
+      handler;
+  in
+    stage {
+      name = "mosdepth-depth";
+      buildInputs = with pkgs; [mosdepth];
+      buildCommand = ''
+        mkdir $out
+        ln -s ${input} input.bam
+        ln -s ${bionix.samtools.index indexAttrs input} input.bam.bai
+        mosdepth -t $NIX_BUILD_CORES \
+          ${optionalString (targets != null) (handleTarget targets)} \
+          ${optionalString (flags != null) flags} $out/out input.bam
+      '';
+      passthru.multicore = true;
+    }