implement types

1 files changed, 11 insertions, 4 deletions

diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index ca9e6a8..0d0f7d8 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -12,12 +12,18 @@
 
 with nixpkgs;
 with lib;
+with bionix.types;
+with bionix.compression;
 
-stdenv.mkDerivation {
+let
+  fa = f: matchFiletype "bwa-ref" { fa = _: f; } f;
+  fq = f: matchFiletype "bwa-input" { fq = _: f; } f;
+
+in stdenv.mkDerivation {
   name = "bwa-mem";
   buildInputs = [ bwa bc ] ++ optional bamOutput samtools;
   buildCommand = ''
-    ln -s ${ref.seq} ref.fa
+    ln -s ${fa ref} ref.fa
     for f in ${bionix.bwa.index indexAttrs ref}/* ; do
       ln -s $f
     done
@@ -26,9 +32,10 @@ stdenv.mkDerivation {
       >&2 echo "not enough build cores"
       exit 1
     fi
-    bwa mem ${optionalString (flags != null) flags} -t $cores ref.fa ${input1} \
-      ${optionalString (input2 != null) input2} \
+    bwa mem ${optionalString (flags != null) flags} -t $cores ref.fa ${fq input1} \
+      ${optionalString (input2 != null) (fq input2)} \
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = option-sort.none;} else filetype.sam {ref = ref; sorting = option-sort.none;};
 }