refactor, add mosdepth, and fixes for bwa

1 files changed, 4 insertions, 37 deletions

diff --git a/tools/strelka.nix b/tools/strelka.nix
index ec7a764..a115740 100644
--- a/tools/strelka.nix
+++ b/tools/strelka.nix
@@ -1,40 +1,7 @@
-{ stdenv
-, callPackage
-, lib
-, strelka
-, ref
-, index ? callPackage ./samtools-faidx.nix {}
-, bamIndex ? callPackage ./samtools-index.nix {}
-, flags ? null
-}:
+{ bionix, nixpkgs }:
 
-{normal, tumour}:
+with nixpkgs;
 
-with lib;
-
-let
-  filename = path: last (splitString "/" path);
-  inputs = [ normal tumour ];
-
-in stdenv.mkDerivation {
-  name = "strelka";
-  buildInputs = [ strelka ];
-  buildCommand = ''
-    ln -s ${ref} ref.fa
-    ln -s ${index 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}
-
-    configureStrelkaSomaticWorkflow.py \
-      --normalBam ${filename normal}.bam \
-      --tumourBam ${filename tumour}.bam \
-      --ref ref.fa \
-      --runDir $TMPDIR
-
-    ./runWorkflow.py \
-      -m local \
-      -j $NIX_BUILD_CORES
-
-    cp -r results $out
-   '';
+{
+  call = attrs: callPackage ./strelka-call.nix attrs;
 }