sambamba: init

4 files changed, 73 insertions, 0 deletions

diff --git a/default.nix b/default.nix
index b04fdc2..32aa232 100644
--- a/default.nix
+++ b/default.nix
@@ -33,6 +33,7 @@ let
     platypus = callBionix ./tools/platypus.nix {};
     ref = callBionix ./lib/references.nix {};
     samtools = callBionix ./tools/samtools.nix {};
+    sambamba = callBionix ./tools/sambamba.nix {};
     snap = callBionix ./tools/snap.nix {};
     snpeff = callBionix ./tools/snpeff.nix {};
     strelka = callBionix ./tools/strelka.nix {};
diff --git a/tools/sambamba-generic.nix b/tools/sambamba-generic.nix
new file mode 100644
index 0000000..a6be65c
--- /dev/null
+++ b/tools/sambamba-generic.nix
@@ -0,0 +1,28 @@
+{ bionix
+, flags ? null
+, tool
+, region ? null
+}:
+
+input:
+
+with bionix;
+with lib;
+
+let
+  inherit (bionix.types) matchFiletype coordSort matchFileSorting;
+in
+
+assert (matchFiletype "sambamba-${tool}" { bam = _: true; } input);
+
+stage {
+  name = "sambamba-${tool}";
+  buildInputs = [ pkgs.sambamba ];
+  buildCommand = ''
+    sambamba ${tool} -t $NIX_BUILD_CORES \
+      ${optionalString (flags != null) flags} \
+      ${if tool == "merge" then "$out ${concatStringsSep " " input}" else if tool == "slice" then "${input} ${region} > $out" else if tool == "flagstat" then "${input} > $out" else "${input} $out"}
+  '';
+  passthru.filetype = if tool == "flagstat" || tool == "index" then null else if tool == "merge" then (head input).filetype else input.filetype;
+  passthru.multicore = true;
+}
diff --git a/tools/sambamba-sort.nix b/tools/sambamba-sort.nix
new file mode 100644
index 0000000..efdd261
--- /dev/null
+++ b/tools/sambamba-sort.nix
@@ -0,0 +1,29 @@
+{ bionix
+, nameSort ? false
+, flags ? null
+}:
+
+input:
+
+with bionix;
+with lib;
+
+let
+  inherit (bionix.types) matchFiletype coordSort matchFileSorting;
+in
+
+assert (matchFiletype "sambamba-sort" { bam = _: true; } input);
+
+stage {
+  name = "sambamba-sort";
+  buildInputs = [ pkgs.sambamba ];
+  buildCommand = ''
+    sambamba sort -t $NIX_BUILD_CORES \
+      ${optionalString nameSort "-n"} \
+      ${optionalString (flags != null) flags} \
+      -o $out \
+      ${input}
+  '';
+  passthru.filetype = if nameSort then bionix.types.nameSort input.filetype else coordSort input.filetype;
+  passthru.multicore = true;
+}
diff --git a/tools/sambamba.nix b/tools/sambamba.nix
new file mode 100644
index 0000000..552e6e3
--- /dev/null
+++ b/tools/sambamba.nix
@@ -0,0 +1,15 @@
+{ bionix }:
+
+with bionix;
+
+let
+  gen = callBionixE ./sambamba-generic.nix;
+
+in {
+  sort = callBionixE ./sambamba-sort.nix;
+  index = def gen {tool = "index"; };
+  merge = def gen {tool = "merge"; };
+  slice = def gen {tool = "slice"; };
+  flagstat = def gen {tool = "flagstat"; };
+  markdup = def gen {tool = "markdup"; };
+}