implement types

1 files changed, 13 insertions, 2 deletions

diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix
index 2de579e..ab9d603 100644
--- a/tools/samtools-sort.nix
+++ b/tools/samtools-sort.nix
@@ -2,6 +2,7 @@
 , nixpkgs
 , nameSort ? false
 , flags ? null
+, outfmt ? null
 }:
 
 input:
@@ -9,10 +10,20 @@ input:
 with nixpkgs;
 with lib;
 
-stdenv.mkDerivation {
+let
+  inherit (bionix.types) matchFiletype coordSort;
+in
+
+assert (matchFiletype "samtools-sort" { bam = _: true; sam = _: true; cram = _: true; } input);
+
+let
+  outfmtR = if outfmt != null then outfmt input else input.filetype;
+  outFmtFlags = matchFiletype "samtools-sort-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = ref: "-O CRAM -T ${ref}"; } {filetype = outfmtR;};
+in stdenv.mkDerivation {
   name = "samtools-sort";
   buildInputs = [ samtools ];
   buildCommand = ''
-    samtools sort -@ $NIX_BUILD_CORES ${optionalString nameSort "-n"} ${optionalString (flags != null) flags} ${input} > $out
+    samtools sort -@ $NIX_BUILD_CORES ${optionalString nameSort "-n"} ${outFmtFlags} ${optionalString (flags != null) flags} ${input} > $out
   '';
+  passthru.filetype = if nameSort then bionix.types.nameSort outfmtR else coordSort outfmtR;
 }