1 files changed, 52 insertions, 58 deletions
diff --git a/tools/octopus-call.nix b/tools/octopus-call.nix
index 8a78f01..6851971 100644
--- a/tools/octopus-call.nix
+++ b/tools/octopus-call.nix
@@ -1,73 +1,67 @@
-{ bionix
-, fast ? false
-, very-fast ? false
-, max-genotypes ? null
-, targets ? null
-, faidxAttrs ? { }
-, indexAttrs ? { }
-, flags ? ""
+{
+  bionix,
+  fast ? false,
+  very-fast ? false,
+  max-genotypes ? null,
+  targets ? null,
+  faidxAttrs ? {},
+  indexAttrs ? {},
+  flags ? "",
 }:
-
 assert !fast || !very-fast;
 assert max-genotypes == null || max-genotypes > 0;
-
 with bionix;
 with lib;
 with types;
+  inputs: let
+    getref = matchFiletype "octopus-call" {
+      bam = {ref, ...}: ref;
+      cram = {ref, ...}: ref;
+    };
+    refs = map getref inputs;
+    ref = head refs;
 
-inputs:
-
-let
-  getref = matchFiletype "octopus-call" { bam = { ref, ... }: ref; cram = { ref, ... }: ref; };
-  refs = map getref inputs;
-  ref = head refs;
-
-
-  handleTarget = x:
-    let
+    handleTarget = x: let
       type = builtins.typeOf x;
-      handler = handlers."${type}" or (builtins.throw "octopus-callSomatic:unhandled target type:${type}");
+      handler = handlers."${type}" or (builtins.throw "octopus-call:unhandled target type:${type}");
       handlers = {
         string = "-T '${x}'";
-        list =
-          let file = pkgs.writeText "regions.txt" (concatStringsSep "\n" x);
-          in "-t ${file}";
+        list = let
+          file = pkgs.writeText "regions.txt" (concatStringsSep "\n" x);
+        in "-t ${file}";
         path = "-t ${x}";
         set = "-t ${x}";
       };
     in
-    handler;
-
-
-in
-
-assert (length (unique refs) == 1);
-
-stage {
-  name = "octopus-call";
-  buildInputs = with pkgs; [ octopus-caller ];
-  outputs = [ "out" "evidence" ];
-  buildCommand = ''
-    ln -s ${ref} ref.fa
-    ln -s ${samtools.faidx faidxAttrs ref} ref.fai
-    ${concatMapStringsSep "\n" (i: ''
-      ln -s ${i} $(basename ${i}).bam
-      ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai
-    '') inputs}
-    ${optionalString (length inputs > 1) "mkdir $evidence"}
-    octopus -R ref.fa -I *.bam -o $out \
-      --bamout $evidence \
-      --threads=$NIX_BUILD_CORES \
-      ${optionalString fast "--fast"} \
-      ${optionalString very-fast "--very-fast"} \
-      ${optionalString (max-genotypes != null) "--max-genotypes ${toString max-genotypes}"} \
-      ${optionalString (targets != null) (handleTarget targets)} \
-      ${flags}
+      handler;
+  in
+    assert (length (unique refs) == 1);
+      stage {
+        name = "octopus-call";
+        buildInputs = with pkgs; [octopus-caller];
+        outputs = ["out" "evidence"];
+        buildCommand = ''
+          ln -s ${ref} ref.fa
+          ln -s ${samtools.faidx faidxAttrs ref} ref.fai
+          ${concatMapStringsSep "\n" (i: ''
+              ln -s ${i} $(basename ${i}).bam
+              ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai
+            '')
+            inputs}
+          ${optionalString (length inputs > 1) "mkdir $evidence"}
+          octopus -R ref.fa -I *.bam -o $out \
+            --bamout $evidence \
+            --threads=$NIX_BUILD_CORES \
+            ${optionalString fast "--fast"} \
+            ${optionalString very-fast "--very-fast"} \
+            ${optionalString (max-genotypes != null) "--max-genotypes ${toString max-genotypes}"} \
+            ${optionalString (targets != null) (handleTarget targets)} \
+            ${flags}
 
-    # Strip out octopus ARGV
-    sed -i '/^##octopus=/d' $out
-  '';
-  passthru.filetype = filetype.vcf { inherit ref; };
-  passthru.multicore = true;
-  stripStorePaths = false;
-}
+          # Strip out octopus ARGV
+          sed -i '/^##octopus=/d' $out
+        '';
+        passthru.filetype = filetype.vcf {inherit ref;};
+        passthru.multicore = true;
+        stripStorePaths = false;
+      }