1 files changed, 7 insertions, 8 deletions
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index ec7a764..e7fbb58 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -1,15 +1,14 @@
-{ stdenv
-, callPackage
-, lib
-, strelka
+{ bionix
+, nixpkgs
 , ref
-, index ? callPackage ./samtools-faidx.nix {}
-, bamIndex ? callPackage ./samtools-index.nix {}
+, indexAttrs ? {}
+, bamIndexAttrs ? {}
 , flags ? null
 }:
 
 {normal, tumour}:
 
+with nixpkgs;
 with lib;
 
 let
@@ -21,9 +20,9 @@ in stdenv.mkDerivation {
   buildInputs = [ strelka ];
   buildCommand = ''
     ln -s ${ref} ref.fa
-    ln -s ${index ref} ref.fa.fai
+    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 ${bamIndex p} ${filename p}.bai") inputs}
+    ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
 
     configureStrelkaSomaticWorkflow.py \
       --normalBam ${filename normal}.bam \