refactor, add mosdepth, and fixes for bwa

1 files changed, 40 insertions, 0 deletions

diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
new file mode 100644
index 0000000..5a2772e
--- /dev/null
+++ b/tools/bwa-mem.nix
@@ -0,0 +1,40 @@
+{ stdenv
+, callPackage
+, lib
+, bc
+, bwa
+, samtools ? null
+, ref
+, bamOutput ? true
+, flags ? null
+}:
+
+{ input1
+, input2 ? null
+}:
+
+assert bamOutput -> samtools != null;
+
+with lib;
+
+let index = callPackage ./bwa-index.nix { inherit bwa stdenv lib; } ref;
+
+in stdenv.mkDerivation {
+  name = "bwa-mem";
+  buildInputs = [ bwa bc ] ++ optional bamOutput samtools;
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    for f in ${index}/* ; do
+      ln -s $f
+    done
+    cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
+    if [[ $cores -lt 1 ]] ; then
+      >&2 echo "not enough build cores"
+      exit 1
+    fi
+    bwa mem ${optionalString (flags != null) flags} -t $cores ref.fa ${input1} \
+      ${optionalString (input2 != null) input2} \
+      ${optionalString bamOutput "| samtools view -b"} \
+      > $out
+  '';
+}