refactor, add mosdepth, and fixes for bwa

1 files changed, 40 insertions, 0 deletions

diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
new file mode 100644
index 0000000..ec7a764
--- /dev/null
+++ b/tools/strelka-call.nix
@@ -0,0 +1,40 @@
+{ stdenv
+, callPackage
+, lib
+, strelka
+, ref
+, index ? callPackage ./samtools-faidx.nix {}
+, bamIndex ? callPackage ./samtools-index.nix {}
+, flags ? null
+}:
+
+{normal, tumour}:
+
+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
+   '';
+}