refactor, add mosdepth, and fixes for bwa

1 files changed, 33 insertions, 0 deletions

diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
new file mode 100644
index 0000000..3e150d2
--- /dev/null
+++ b/tools/platypus-callVariants.nix
@@ -0,0 +1,33 @@
+{ stdenv
+, callPackage
+, lib
+, platypus
+, ref
+, index ? callPackage ./samtools-faidx.nix {}
+, bamIndex ? callPackage ./samtools-index.nix {}
+, flags ? null
+}:
+
+inputs:
+
+with lib;
+
+let filename = path: last (splitString "/" path);
+
+in stdenv.mkDerivation {
+  name = "platypus";
+  buildInputs = [ platypus ];
+  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} ${filename p}.bai") inputs}
+    ls -l
+    platypus callVariants \
+      --nCPU=$NIX_BUILD_CORES \
+      --refFile=ref.fa \
+      ${optionalString (flags != null) flags} \
+      -o $out \
+      --bamFiles=${concatMapStringsSep "," (p: "${filename p}.bam") inputs}
+  '';
+}