Merge branch 'master' of https://github.com/PapenfussLab/bionix

3 files changed, 28 insertions, 22 deletions

diff --git a/test.nix b/test.nix
index 8126e63..9851310 100644
--- a/test.nix
+++ b/test.nix
@@ -1,28 +1,35 @@
-{pkgs ? import <nixpkgs> {}}:
+{pkgs ? import <nixpkgs> {}
+,bionix ? import <bionix> {}}:
 
 with pkgs;
 with lib;
+with bionix;
 
 let
-  ref = ./example/ref.fa;
-  alignWithRG = rg: callPackage ./tools/bwa.nix { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
-  sort = callPackage ./tools/samtools-sort.nix { };
-  callVariants = callPackage ./tools/platypus.nix { inherit ref; };
+  inherit (types) filetype tagFiletype;
 
-  samples = [ {name = "mysample1"; files = {input1 = ./example/sample1-1.fq; input2 = ./example/sample1-2.fq;};}
-              {name = "mysample2"; files = {input1 = ./example/sample2-1.fq; input2 = ./example/sample2-1.fq;};} ];
+  fetchLocal = path: stdenv.mkDerivation {
+    name = baseNameOf path;
+    buildCommand = "ln -s ${path} $out";
+  };
+  tagfq = path: tagFiletype (filetype.fq {}) (fetchLocal path);
+  tagfa = path: tagFiletype (filetype.fa {}) (fetchLocal path);
 
-  alignments = map (i: sort (alignWithRG i.name i.files)) samples;
-  variants = callVariants alignments;
+  ref = tagfa ./example/ref.fa;
+  alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
 
-  testNaming = stdenv.mkDerivation {
-    name = "test-naming";
-    buildCommand = ''
-      mkdir $out
-      ln -s ${variants} $out/myfancyname
-      mkdir $out/alignments
-      ${concatStringsSep "\n" (zipListsWith (s: a: "ln -s ${a} $out/alignments/${s.name}.bam") samples alignments)}
-    '';
-  };
+  samples = [ {name = "mysample1"; files = {input1 = tagfq ./example/sample1-1.fq; input2 = tagfq ./example/sample1-2.fq;};}
+              {name = "mysample2"; files = {input1 = tagfq ./example/sample2-1.fq; input2 = tagfq ./example/sample2-1.fq;};} ];
+
+  alignments = map (i: samtools.sort {} (alignWithRG i.name i.files)) samples;
+  variants = platypus.call {} alignments;
 
-in testNaming
+in stdenv.mkDerivation {
+  name = "myproject";
+  buildCommand = ''
+    mkdir $out
+    ln -s ${variants} $out/platypus.vcf
+    mkdir $out/alignments
+    ${concatStringsSep "\n" (zipListsWith (s: a: "ln -s ${a} $out/alignments/${s.name}.bam") samples alignments)}
+  '';
+}
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 0d0f7d8..3208e48 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -29,8 +29,7 @@ in stdenv.mkDerivation {
     done
     cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
     if [[ $cores -lt 1 ]] ; then
-      >&2 echo "not enough build cores"
-      exit 1
+      cores=1
     fi
     bwa mem ${optionalString (flags != null) flags} -t $cores ref.fa ${fq input1} \
       ${optionalString (input2 != null) (fq input2)} \
diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
index a3e3a65..a57aa83 100644
--- a/tools/platypus-callVariants.nix
+++ b/tools/platypus-callVariants.nix
@@ -14,7 +14,7 @@ with bionix.types;
 
 let
   filename = path: last (splitString "/" path);
-  getref = f: matchFiletype "platypus-callVariants" { bam = r: r; } f;
+  getref = f: matchFiletype "platypus-callVariants" { bam = {ref, ...}: ref; } f;
   refs = map getref inputs;
   ref = head refs;
 in