22 files changed, 110 insertions, 111 deletions
diff --git a/default.nix b/default.nix
index 10d2249..9f96a9d 100644
--- a/default.nix
+++ b/default.nix
@@ -2,18 +2,21 @@
 
 let
   bionix = nixpkgs.lib.makeExtensible (self:
-    let callBionix = file: import file { bionix = self; nixpkgs = nixpkgs; };
-    in with self; {
-      bwa = callBionix ./tools/bwa.nix;
-      crumble = callBionix ./tools/crumble.nix;
-      fastqc = callBionix ./tools/fastqc.nix;
-      gridss = callBionix ./tools/gridss.nix;
-      mosdepth = callBionix ./tools/mosdepth.nix;
-      platypus = callBionix ./tools/platypus.nix;
-      samtools = callBionix ./tools/samtools.nix;
-      strelka = callBionix ./tools/strelka.nix;
+  let callBionix = file: attrs: import file ({ bionix = self; nixpkgs = nixpkgs; } // attrs);
+  in with self; {
+      callBionix = callBionix;
+      id = x: x;
+
+      bwa = callBionix ./tools/bwa.nix {};
+      crumble = callBionix ./tools/crumble.nix {};
+      fastqc = callBionix ./tools/fastqc.nix {};
+      gridss = callBionix ./tools/gridss.nix {};
+      mosdepth = callBionix ./tools/mosdepth.nix {};
+      platypus = callBionix ./tools/platypus.nix {};
+      samtools = callBionix ./tools/samtools.nix {};
+      strelka = callBionix ./tools/strelka.nix {};
 
       qsub = nixpkgs.callPackage ./lib/qsub.nix {};
-      ref = callBionix ./lib/references.nix;
+      ref = callBionix ./lib/references.nix {};
   });
 in bionix
diff --git a/test-tnpair.nix b/test-tnpair.nix
index ef2af1b..77b5727 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -1,11 +1,19 @@
 with (import <nixpkgs> {});
-with (import <bionix> {});
 with lib;
 
 let
+  bionix = (import <bionix> {}).extend (self: super: {
+    bwa = super.bwa // { index = attrs: super.bwa.index ({ flags = "-a is" ; } // attrs); };
+  });
+
+in
+
+with bionix;
+
+let
   ref = ./example/ref.fa;
   alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
-  sort = samtools.sort { };
+  sort = samtools.sort {};
   flagstat = samtools.flagstat {};
   check = fastqc.check {};
   callVariants = strelka.call { inherit ref; };
diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix
index 3329221..3f9d385 100644
--- a/tools/bwa-index.nix
+++ b/tools/bwa-index.nix
@@ -1,11 +1,11 @@
-{ stdenv
-, lib
-, bwa
+{ bionix
+, nixpkgs
 , flags ? null
 }:
 
 ref:
 
+with nixpkgs;
 with lib;
 
 stdenv.mkDerivation {
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 9af3992..6e83a6d 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -1,21 +1,16 @@
-{ stdenv
-, callPackage
-, lib
-, bc
-, bwa
-, index ? callPackage ./bwa-index.nix { inherit bwa stdenv lib; }
-, samtools ? null
+{ bionix
+, nixpkgs
 , ref
 , bamOutput ? true
 , flags ? null
+, indexAttrs ? {}
 }:
 
 { input1
 , input2 ? null
 }:
 
-assert bamOutput -> samtools != null;
-
+with nixpkgs;
 with lib;
 
 stdenv.mkDerivation {
@@ -23,7 +18,7 @@ stdenv.mkDerivation {
   buildInputs = [ bwa bc ] ++ optional bamOutput samtools;
   buildCommand = ''
     ln -s ${ref} ref.fa
-    for f in ${index ref}/* ; do
+    for f in ${bionix.bwa.index indexAttrs ref}/* ; do
       ln -s $f
     done
     cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
diff --git a/tools/bwa.nix b/tools/bwa.nix
index df61cba..1d5215f 100644
--- a/tools/bwa.nix
+++ b/tools/bwa.nix
@@ -1,8 +1,8 @@
 { bionix, nixpkgs }:
 
-with nixpkgs;
+with bionix;
 
 {
-  align = attrs: callPackage ./bwa-mem.nix attrs;
-  index = attrs: callPackage ./bwa-index.nix attrs;
+  align = callBionix ./bwa-mem.nix;
+  index = callBionix ./bwa-index.nix;
 }
diff --git a/tools/crumble-toCram.nix b/tools/crumble-toCram.nix
index 6b2431f..2544e17 100644
--- a/tools/crumble-toCram.nix
+++ b/tools/crumble-toCram.nix
@@ -1,15 +1,15 @@
-{ stdenv
-, lib
-, callPackage
-, crumble ? callPackage ./crumble-app.nix {}
-, flags ? null}:
+{ bionix
+, nixpkgs
+, flags ? null
+}:
 
+with nixpkgs;
 with lib;
 
 input:
 
 stdenv.mkDerivation {
   name = "crumble";
-  buildInputs = [ crumble ];
+  buildInputs = [ bionix.crumble.crumble ];
   buildCommand = "crumble ${optionalString (flags != null) flags} ${input} $out";
 }
diff --git a/tools/crumble.nix b/tools/crumble.nix
index 4798329..fb48c8f 100644
--- a/tools/crumble.nix
+++ b/tools/crumble.nix
@@ -1,7 +1,9 @@
 { bionix, nixpkgs }:
 
 with nixpkgs;
+with bionix;
 
 {
-  toCram = attrs: callPackage ./crumble-toCram.nix attrs;
+  crumble = callPackage ./crumble-app.nix {};
+  toCram = callBionix ./crumble-toCram.nix;
 }
diff --git a/tools/fastqc-check.nix b/tools/fastqc-check.nix
index 1d9993a..17d6183 100644
--- a/tools/fastqc-check.nix
+++ b/tools/fastqc-check.nix
@@ -1,16 +1,16 @@
-{ stdenv
-, lib
-, callPackage
-, fastqc ? callPackage ./fastqc-app.nix {}
-, flags ? null}:
+{ bionix
+, nixpkgs
+, flags ? null
+}:
 
+with nixpkgs;
 with lib;
 
 input:
 
 stdenv.mkDerivation {
   name = "fastqc-check";
-  buildInputs = [ fastqc ];
+  buildInputs = [ bionix.fastqc.fastqc ];
   buildCommand = ''
     mkdir $out
     fastqc \
diff --git a/tools/fastqc.nix b/tools/fastqc.nix
index 2034c91..1661e95 100644
--- a/tools/fastqc.nix
+++ b/tools/fastqc.nix
@@ -1,7 +1,9 @@
 { bionix, nixpkgs }:
 
 with nixpkgs;
+with bionix;
 
 {
-  check = attrs: callPackage ./fastqc-check.nix attrs;
+  fastqc = callPackage ./fastqc-app.nix {};
+  check = callBionix ./fastqc-check.nix;
 }
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index 9d78896..e431560 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -1,15 +1,11 @@
-{ stdenv
-, lib
-, callPackage
-, fetchurl
-, jre
-, R
-, bwa
+{ bionix
+, nixpkgs
 , ref
 , blacklist ? null
-, bwaIndex ? callPackage ./bwa-index.nix { inherit stdenv bwa lib; }
-, faidx ? callPackage ./samtools-faidx.nix { inherit stdenv; }
-, flags ? null}:
+, bwaIndexAttrs ? {}
+, faidxAttrs ? {}
+, flags ? null
+}:
 
 with lib;
 
@@ -24,8 +20,8 @@ stdenv.mkDerivation rec {
   };
   buildCommand = ''
     ln -s ${ref} ref.fa
-    ln -s ${faidx ref} ref.fa.fai
-    for f in ${bwaIndex ref}/*; do
+    ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
+    for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
       ln -s $f
     done
     mkdir $out
diff --git a/tools/gridss.nix b/tools/gridss.nix
index fa52606..edf9f57 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -1,7 +1,7 @@
 {bionix, nixpkgs}:
 
-with nixpkgs;
+with bionix;
 
 {
-  callVariants = attrs: callPackage ./gridss-callVariants.nix attrs;
+  callVariants = callBiolnix ./gridss-callVariants.nix;
 }
diff --git a/tools/mosdepth-depth.nix b/tools/mosdepth-depth.nix
index be28aaf..7043c43 100644
--- a/tools/mosdepth-depth.nix
+++ b/tools/mosdepth-depth.nix
@@ -1,10 +1,10 @@
-{ stdenv
-, lib
-, callPackage
-, mosdepth
-, index ? callPackage ./samtools-index.nix {}
-, flags ? null}:
+{ bionix
+, nixpkgs
+, indexAttrs ? {}
+, flags ? null
+}:
 
+with nixpkgs;
 with lib;
 
 input:
@@ -15,7 +15,7 @@ stdenv.mkDerivation {
   buildCommand = ''
     mkdir $out
     ln -s ${input} input.bam
-    ln -s ${index input} input.bam.bai
+    ln -s ${bionix.samtools.index indexAttrs input} input.bam.bai
     mosdepth -t $NIX_BUILD_CORES ${optionalString (flags != null) flags} $out/out input.bam
   '';
 }
diff --git a/tools/mosdepth-plot.nix b/tools/mosdepth-plot.nix
index e6d2c7d..f15e099 100644
--- a/tools/mosdepth-plot.nix
+++ b/tools/mosdepth-plot.nix
@@ -1,9 +1,9 @@
-{ stdenv
-, lib
-, mosdepth
-, python
-, flags ? null}:
+{ bionix
+, nixpkgs
+, flags ? null
+}:
 
+with nixpkgs;
 with lib;
 
 { inputs
diff --git a/tools/mosdepth.nix b/tools/mosdepth.nix
index 447e530..ff940a5 100644
--- a/tools/mosdepth.nix
+++ b/tools/mosdepth.nix
@@ -1,8 +1,8 @@
 { bionix, nixpkgs }:
 
-with nixpkgs;
+with bionix;
 
 {
-  depth = attrs: callPackage ./mosdepth-depth.nix attrs;
-  plot = attrs: callPackage ./mosdepth-plot.nix attrs;
+  depth = callBionix ./mosdepth-depth.nix;
+  plot = callBionix ./mosdepth-plot.nix;
 }
diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
index 3e150d2..c0204dc 100644
--- a/tools/platypus-callVariants.nix
+++ b/tools/platypus-callVariants.nix
@@ -1,10 +1,8 @@
-{ stdenv
-, callPackage
-, lib
-, platypus
+{ bionix
+, nixpkgs
 , ref
-, index ? callPackage ./samtools-faidx.nix {}
-, bamIndex ? callPackage ./samtools-index.nix {}
+, indexAttrs ? {}
+, bamIndexAttrs ? {}
 , flags ? null
 }:
 
@@ -19,9 +17,9 @@ in stdenv.mkDerivation {
   buildInputs = [ platypus ];
   buildCommand = ''
     ln -s ${ref} ref.fa
-    ln -s ${index ref} ref.fa.fai
+    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 ${bamIndex p} ${filename p}.bai") inputs}
+    ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
     ls -l
     platypus callVariants \
       --nCPU=$NIX_BUILD_CORES \
diff --git a/tools/samtools-faidx.nix b/tools/samtools-faidx.nix
index a399857..72116b8 100644
--- a/tools/samtools-faidx.nix
+++ b/tools/samtools-faidx.nix
@@ -1,12 +1,11 @@
-{ stdenv
-, callPackage
-, lib
-, samtools
+{ bionix
+, nixpkgs
 , flags ? null
 }:
 
 input:
 
+with nixpkgs;
 with lib;
 
 stdenv.mkDerivation {
diff --git a/tools/samtools-flagstat.nix b/tools/samtools-flagstat.nix
index 790eeb4..ae36c94 100644
--- a/tools/samtools-flagstat.nix
+++ b/tools/samtools-flagstat.nix
@@ -1,11 +1,10 @@
-{ stdenv
-, callPackage
-, lib
-, samtools
+{ bionix
+, nixpkgs
 }:
 
 input:
 
+with nixpkgs;
 with lib;
 
 stdenv.mkDerivation {
diff --git a/tools/samtools-index.nix b/tools/samtools-index.nix
index 2fd066f..4e09dc7 100644
--- a/tools/samtools-index.nix
+++ b/tools/samtools-index.nix
@@ -1,12 +1,11 @@
-{ stdenv
-, callPackage
-, lib
-, samtools
+{ bionix
+, nixpkgs
 , flags ? null
 }:
 
 input:
 
+with nixpkgs;
 with lib;
 
 stdenv.mkDerivation {
diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix
index 1a79c9f..2de579e 100644
--- a/tools/samtools-sort.nix
+++ b/tools/samtools-sort.nix
@@ -1,13 +1,12 @@
-{ stdenv
-, callPackage
-, lib
-, samtools
+{ bionix
+, nixpkgs
 , nameSort ? false
 , flags ? null
 }:
 
 input:
 
+with nixpkgs;
 with lib;
 
 stdenv.mkDerivation {
diff --git a/tools/samtools.nix b/tools/samtools.nix
index 77e3815..6b08c6e 100644
--- a/tools/samtools.nix
+++ b/tools/samtools.nix
@@ -1,10 +1,10 @@
 { bionix, nixpkgs }:
 
-with nixpkgs;
+with bionix;
 
 {
-  faidx = attrs: callPackage ./samtools-faidx.nix attrs;
-  flagstat = attrs: callPackage ./samtools-flagstat.nix attrs;
-  index = attrs: callPackage ./samtools-index.nix attrs;
-  sort = attrs: callPackage ./samtools-sort.nix attrs;
+  faidx = callBionix ./samtools-faidx.nix;
+  flagstat = callBionix ./samtools-flagstat.nix;
+  index = callBionix ./samtools-index.nix;
+  sort = callBionix ./samtools-sort.nix;
 }
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index ec7a764..e7fbb58 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -1,15 +1,14 @@
-{ stdenv
-, callPackage
-, lib
-, strelka
+{ bionix
+, nixpkgs
 , ref
-, index ? callPackage ./samtools-faidx.nix {}
-, bamIndex ? callPackage ./samtools-index.nix {}
+, indexAttrs ? {}
+, bamIndexAttrs ? {}
 , flags ? null
 }:
 
 {normal, tumour}:
 
+with nixpkgs;
 with lib;
 
 let
@@ -21,9 +20,9 @@ in stdenv.mkDerivation {
   buildInputs = [ strelka ];
   buildCommand = ''
     ln -s ${ref} ref.fa
-    ln -s ${index ref} ref.fa.fai
+    ln -s ${bionix.samtools.faidx indexAttrs 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}
+    ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
 
     configureStrelkaSomaticWorkflow.py \
       --normalBam ${filename normal}.bam \
diff --git a/tools/strelka.nix b/tools/strelka.nix
index a115740..767c270 100644
--- a/tools/strelka.nix
+++ b/tools/strelka.nix
@@ -1,7 +1,7 @@
 { bionix, nixpkgs }:
 
-with nixpkgs;
+with bionix;
 
 {
-  call = attrs: callPackage ./strelka-call.nix attrs;
+  call = callBionix ./strelka-call.nix;
 }