1 files changed, 29 insertions, 0 deletions
diff --git a/tools/sambamba-sort.nix b/tools/sambamba-sort.nix
new file mode 100644
index 0000000..efdd261
--- /dev/null
+++ b/tools/sambamba-sort.nix
@@ -0,0 +1,29 @@
+{ bionix
+, nameSort ? false
+, flags ? null
+}:
+
+input:
+
+with bionix;
+with lib;
+
+let
+  inherit (bionix.types) matchFiletype coordSort matchFileSorting;
+in
+
+assert (matchFiletype "sambamba-sort" { bam = _: true; } input);
+
+stage {
+  name = "sambamba-sort";
+  buildInputs = [ pkgs.sambamba ];
+  buildCommand = ''
+    sambamba sort -t $NIX_BUILD_CORES \
+      ${optionalString nameSort "-n"} \
+      ${optionalString (flags != null) flags} \
+      -o $out \
+      ${input}
+  '';
+  passthru.filetype = if nameSort then bionix.types.nameSort input.filetype else coordSort input.filetype;
+  passthru.multicore = true;
+}