implement types

1 files changed, 15 insertions, 5 deletions

diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
index 7b68b28..a3e3a65 100644
--- a/tools/platypus-callVariants.nix
+++ b/tools/platypus-callVariants.nix
@@ -1,6 +1,5 @@
 { bionix
 , nixpkgs
-, ref
 , indexAttrs ? {}
 , bamIndexAttrs ? {}
 , flags ? null
@@ -8,16 +7,26 @@
 
 inputs:
 
+with nixpkgs;
 with lib;
+with bionix.types;
 
-let filename = path: last (splitString "/" path);
 
-in stdenv.mkDerivation {
+let
+  filename = path: last (splitString "/" path);
+  getref = f: matchFiletype "platypus-callVariants" { bam = r: r; } f;
+  refs = map getref inputs;
+  ref = head refs;
+in
+
+assert (length (unique refs) == 1);
+
+stdenv.mkDerivation {
   name = "platypus";
   buildInputs = [ platypus ];
   buildCommand = ''
-    ln -s ${ref.seq} ref.fa
-    ln -s ${bionix.samtools.faix indexAttrs ref} ref.fa.fai
+    ln -s ${ref} ref.fa
+    ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
     ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
     ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
     ls -l
@@ -28,4 +37,5 @@ in stdenv.mkDerivation {
       -o $out \
       --bamFiles=${concatMapStringsSep "," (p: "${filename p}.bam") inputs}
   '';
+  passthru.filetype = filetype.vcf {ref = ref;};
 }