Refactor references

7 files changed, 8 insertions, 7 deletions

diff --git a/test-tnpair.nix b/test-tnpair.nix
index f8c49ec..3260b7b 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -14,7 +14,7 @@ in
 with bionix;
 
 let
-  ref = ./example/ref.fa;
+  ref = { seq = ./example/ref.fa; };
   alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
   sort = samtools.sort {};
   flagstat = samtools.flagstat {};
diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix
index 3f9d385..48a2556 100644
--- a/tools/bwa-index.nix
+++ b/tools/bwa-index.nix
@@ -12,7 +12,7 @@ stdenv.mkDerivation {
   name = "bwa-index";
   buildInputs = [ bwa ];
   buildCommand = ''
-    ln -s ${ref} ref.fa
+    ln -s ${ref.seq} ref.fa
     bwa index ${optionalString (flags != null) flags} ref.fa
     mkdir $out
     mv ref.fa.* $out
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 6e83a6d..ca9e6a8 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -17,7 +17,7 @@ stdenv.mkDerivation {
   name = "bwa-mem";
   buildInputs = [ bwa bc ] ++ optional bamOutput samtools;
   buildCommand = ''
-    ln -s ${ref} ref.fa
+    ln -s ${ref.seq} ref.fa
     for f in ${bionix.bwa.index indexAttrs ref}/* ; do
       ln -s $f
     done
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index e431560..c313c3f 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
     sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k";
   };
   buildCommand = ''
-    ln -s ${ref} ref.fa
+    ln -s ${ref.seq} ref.fa
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
     for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
       ln -s $f
diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
index c0204dc..7b68b28 100644
--- a/tools/platypus-callVariants.nix
+++ b/tools/platypus-callVariants.nix
@@ -16,7 +16,7 @@ in stdenv.mkDerivation {
   name = "platypus";
   buildInputs = [ platypus ];
   buildCommand = ''
-    ln -s ${ref} ref.fa
+    ln -s ${ref.seq} ref.fa
     ln -s ${bionix.samtools.faix indexAttrs ref} ref.fa.fai
     ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
     ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
diff --git a/tools/samtools-faidx.nix b/tools/samtools-faidx.nix
index 72116b8..bf32bdf 100644
--- a/tools/samtools-faidx.nix
+++ b/tools/samtools-faidx.nix
@@ -9,6 +9,7 @@ with nixpkgs;
 with lib;
 
 stdenv.mkDerivation {
+
   name = "samtools-faidx";
   buildInputs = [ samtools ];
   buildCommand = ''
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index e7fbb58..ecdea84 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -19,8 +19,8 @@ in stdenv.mkDerivation {
   name = "strelka";
   buildInputs = [ strelka ];
   buildCommand = ''
-    ln -s ${ref} ref.fa
-    ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
+    ln -s ${ref.seq} ref.fa
+    ln -s ${bionix.samtools.faidx indexAttrs ref.seq} ref.fa.fai
     ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
     ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}