large refactor

- use bionix.pkgs instead of nixpkgs
- replace stdenv.mkDerivation with stage

46 files changed, 147 insertions, 183 deletions

diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix
index 456747a..67a1169 100644
--- a/tools/bowtie-align.nix
+++ b/tools/bowtie-align.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , ref
 , bamOutput ? true
 , flags ? null
@@ -10,18 +9,18 @@
 , input2 ? null
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
-with bionix.compression;
+with types;
+with compression;
 
 let
   fa = f: matchFiletype "bowtie2-ref" { fa = _: f; } f;
   fq = f: matchFiletype "bowtie2-input" { fq = _: f; gz = matchFiletype' "bowtie2-input" { fq = _: f; }; } f;
 
-in stdenv.mkDerivation {
+in stage {
   name = "bowtie2-align";
-  buildInputs = [ bowtie2 bc ] ++ optional bamOutput samtools;
+  buildInputs = with pkgs; [ bowtie2 bc ] ++ optional bamOutput samtools;
   buildCommand = ''
     cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
     if [[ $cores -lt 1 ]] ; then
diff --git a/tools/bowtie-index.nix b/tools/bowtie-index.nix
index 98e529f..4554ad1 100644
--- a/tools/bowtie-index.nix
+++ b/tools/bowtie-index.nix
@@ -1,20 +1,19 @@
 { bionix
-, nixpkgs
 , flags ? null
 , seed ? 42
 }:
 
 ref:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 assert (matchFiletype "bowtie-index" { fa = _: true; } ref);
 
-stdenv.mkDerivation {
+stage {
   name = "bowtie-index";
-  buildInputs = [ bowtie2 ];
+  buildInputs = with pkgs; [ bowtie2 ];
   buildCommand = ''
     mkdir $out
     bowtie2-build --seed ${toString seed} --threads $NIX_BUILD_CORES ${optionalString (flags != null) flags} ${ref} $out/ref
diff --git a/tools/bowtie.nix b/tools/bowtie.nix
index df8f955..a4439d3 100644
--- a/tools/bowtie.nix
+++ b/tools/bowtie.nix
@@ -1,4 +1,4 @@
-{ bionix, nixpkgs }:
+{ bionix }:
 
 with bionix;
 
diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix
index c879bc4..17b651f 100644
--- a/tools/bwa-index.nix
+++ b/tools/bwa-index.nix
@@ -1,19 +1,18 @@
 { bionix
-, nixpkgs
 , flags ? null
 }:
 
 ref:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 assert (matchFiletype "bwa-index" { fa = _: true; } ref);
 
-stdenv.mkDerivation {
+stage {
   name = "bwa-index";
-  buildInputs = [ bwa ];
+  buildInputs = with pkgs; [ bwa ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     bwa index ${optionalString (flags != null) flags} ref.fa
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 2b3bc64..1427b49 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , ref
 , bamOutput ? true
 , flags ? null
@@ -10,18 +9,18 @@
 , input2 ? null
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
-with bionix.compression;
+with types;
+with compression;
 
 let
   fa = f: matchFiletype "bwa-ref" { fa = _: f; } f;
   fq = f: matchFiletype "bwa-input" { fq = _: f; gz = matchFiletype' "bwa-input" { fq = _: f; }; } f;
 
-in stdenv.mkDerivation {
+in stage {
   name = "bwa-mem";
-  buildInputs = [ bwa bc ] ++ optional bamOutput samtools;
+  buildInputs = with pkgs; [ bwa bc ] ++ optional bamOutput samtools;
   buildCommand = ''
     ln -s ${fa ref} ref.fa
     for f in ${bionix.bwa.index indexAttrs ref}/* ; do
diff --git a/tools/bwa.nix b/tools/bwa.nix
index ea0e6a0..d0ab5ee 100644
--- a/tools/bwa.nix
+++ b/tools/bwa.nix
@@ -1,4 +1,4 @@
-{ bionix, nixpkgs }:
+{ bionix }:
 
 with bionix;
 
diff --git a/tools/compression.nix b/tools/compression.nix
index 4184fec..6e69d7e 100644
--- a/tools/compression.nix
+++ b/tools/compression.nix
@@ -1,6 +1,5 @@
-{bionix, nixpkgs}:
+{bionix}:
 
-with nixpkgs;
 with bionix;
 
 {
@@ -12,11 +11,11 @@ with bionix;
     cram = _: f;
     vcf = _: f;
     bed = _: f;
-    gz = _: types.tagFiletype (types.gunzip f.filetype) (stdenv.mkDerivation {
+    gz = _: types.tagFiletype (types.gunzip f.filetype) (stage {
       name = "gunzip";
       buildCommand = "gunzip < ${f} > $out";
     });
-    bz2 = _: types.tagFiletype (types.bunzip2 f.filetype) (stdenv.mkDerivation {
+    bz2 = _: types.tagFiletype (types.bunzip2 f.filetype) (stage {
       name = "bunzip2";
       buildCommand = "bunzip2 < ${f} > $out";
     });
@@ -24,7 +23,7 @@ with bionix;
 
   gzip = f:
     let
-      gz = (stdenv.mkDerivation {
+      gz = (stage {
         name = "gzip";
         buildCommand = "gzip < ${f} > $out";
         passthru = { filetype = types.filetype.gz f.filetype; };
@@ -42,7 +41,7 @@ with bionix;
 
   bzip2 = f:
     let
-      bz2 = (stdenv.mkDerivation {
+      bz2 = (stage {
         name = "bzip2";
         buildCommand = "bzip2 < ${f} > $out";
         passthru = { filetype = types.filetype.bz2 f.filetype; };
diff --git a/tools/crumble.nix b/tools/crumble.nix
index 6031fca..4256f37 100644
--- a/tools/crumble.nix
+++ b/tools/crumble.nix
@@ -1,8 +1,7 @@
-{ bionix, nixpkgs }:
+{ bionix }:
 
-with nixpkgs;
 with bionix;
 
 {
-  crumble = callPackage ./crumble-app.nix {};
+  crumble = pkgs.callPackage ./crumble-app.nix {};
 }
diff --git a/tools/fastqc-check.nix b/tools/fastqc-check.nix
index 17d6183..d33b987 100644
--- a/tools/fastqc-check.nix
+++ b/tools/fastqc-check.nix
@@ -1,14 +1,13 @@
 { bionix
-, nixpkgs
 , flags ? null
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
 
 input:
 
-stdenv.mkDerivation {
+stage {
   name = "fastqc-check";
   buildInputs = [ bionix.fastqc.fastqc ];
   buildCommand = ''
diff --git a/tools/fastqc.nix b/tools/fastqc.nix
index 6e603b2..5632958 100644
--- a/tools/fastqc.nix
+++ b/tools/fastqc.nix
@@ -1,9 +1,8 @@
-{ bionix, nixpkgs }:
+{ bionix }:
 
-with nixpkgs;
 with bionix;
 
 {
-  fastqc = callPackage ./fastqc-app.nix {};
+  fastqc = pkgs.callPackage ./fastqc-app.nix {};
   check = callBionixE ./fastqc-check.nix;
 }
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index f57bc12..e5cb3ca 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
 , indexAttrs ? {}
@@ -9,9 +8,9 @@
 , heapSize ? "31g"
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 inputs:
 
@@ -36,9 +35,9 @@ in
 assert (all sorted inputs);
 assert (homoRef);
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-assemble";
-  buildInputs = [ jre bwa ];
+  buildInputs = with pkgs; [ jre bwa ];
   buildCommand = ''
     TMPDIR=$(pwd)
     ln -s ${ref} ref.fa
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index d55db23..4117126 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , blacklist ? null
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
@@ -8,9 +7,9 @@
 , heapSize ? "31g"
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 inputs:
 
@@ -22,9 +21,9 @@ in
 
 assert (length (unique refs) == 1);
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-callVariants";
-  buildInputs = [ jre R bwa ];
+  buildInputs = with pkgs; [ jre R bwa ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix
index 17e3c46..37e22f1 100644
--- a/tools/gridss-collectMetrics.nix
+++ b/tools/gridss-collectMetrics.nix
@@ -1,14 +1,13 @@
 { bionix
-, nixpkgs
 , thresholdCoverage ? 10000
 , flags ? null
 , config ? null
 , heapSize ? "1G"
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 input:
 
@@ -17,9 +16,9 @@ let
 in
 
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-collectMetrics";
-  buildInputs = [ jre R ];
+  buildInputs = with pkgs; [ jre R ];
   buildCommand = ''
     mkdir $out
     java -Xmx${heapSize} -cp ${bionix.gridss.jar} \
diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix
index c462461..5b249e7 100644
--- a/tools/gridss-computeSamTags.nix
+++ b/tools/gridss-computeSamTags.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , blacklist ? null
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
@@ -8,9 +7,9 @@
 , heapSize ? "1G"
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 input:
 
@@ -21,9 +20,9 @@ in
 
 assert(sorted);
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-computeSamTags";
-  buildInputs = [ jre ];
+  buildInputs = with pkgs; [ jre ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
diff --git a/tools/gridss-configFile.nix b/tools/gridss-configFile.nix
index 15eba55..d6b600e 100644
--- a/tools/gridss-configFile.nix
+++ b/tools/gridss-configFile.nix
@@ -1,14 +1,15 @@
-{bionix, nixpkgs}:
+{bionix}:
 
-with nixpkgs;
+with bionix;
+with lib;
 
 let
     attrsToGridssConfigString = attrsToGridssConfigStringPrepend "";
 
     attrsToGridssConfigStringPrepend = prepend: attrs:
-        lib.concatStringsSep "\n" (
-            lib.attrValues (
-                lib.mapAttrs
+        concatStringsSep "\n" (
+            attrValues (
+                mapAttrs
                     (name: attr: prepend + (iniLine name attr))
                     attrs));
 
@@ -31,6 +32,6 @@ let
         # Allows for repeated fields (e.g. for adapters):
         list   = name: attr: concatStringsSep "\n" (map (x: iniLine name x) attr);
     };
-in configAttrs: (writeText
+in configAttrs: (pkgs.writeText
         "gridss.properties.override"
         ((attrsToGridssConfigString configAttrs) + "\n"))
diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
index 5fc4c59..f2fab30 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , dictIndexAttrs ? {}
 , faidxAttrs ? {}
 , flags ? null
@@ -9,9 +8,9 @@
 , config ? null
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 input:
 
@@ -20,9 +19,9 @@ let
 in
 
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-extractSVReads";
-  buildInputs = [ jre R ];
+  buildInputs = with pkgs; [ jre R ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index c5d8062..315fbf9 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
 , alignerStreaming ? false
@@ -9,9 +8,9 @@
 
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 input:
 
@@ -19,9 +18,9 @@ let
   ref = matchFiletype "gridss-softClipsToSplitReads" { bam = x: x.ref; } input;
 in
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-softClipsToSplitReads";
-  buildInputs = [ jre bwa ];
+  buildInputs = with pkgs; [ jre bwa ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix
index d3070a8..fc26c5a 100644
--- a/tools/gridss-variants.nix
+++ b/tools/gridss-variants.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
 , indexAttrs ? {}
@@ -11,10 +10,10 @@
 , heapSize ? "4g"
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
-with bionix.gridss;
+with types;
+with gridss;
 
 inputs:
 
@@ -65,9 +64,9 @@ assert (all sorted inputs);
 assert (homoRef);
 
 rec {
-  identify = stdenv.mkDerivation rec {
+  identify = stage rec {
     name = "gridss-identifyVariants";
-    buildInputs = [ jre samtools ];
+    buildInputs = with pkgs; [ jre samtools ];
     buildCommand = mkLinks + ''
       java -Xmx${heapSize} -Dsamjdk.create_index=true \
         -cp ${jar} gridss.IdentifyVariants \
@@ -87,9 +86,9 @@ rec {
     };
   };
 
-  annotate = stdenv.mkDerivation rec {
+  annotate = stage rec {
     name = "gridss-annotateVariants";
-    buildInputs = [ jre ];
+    buildInputs = with pkgs; [ jre ];
     buildCommand = mkLinks + ''
       ln -s ${bionix.gridss.identifyVariants {inherit bwaIndexAttrs faidxAttrs indexAttrs assemblyAttrs collectMetricsAttrs softClipsToSplitReadsAttrs flags config; } inputs} input.vcf
       java -Xmx${heapSize} -Dsamjdk.create_index=true \
diff --git a/tools/gridss.nix b/tools/gridss.nix
index 5bb9484..e8dd304 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -1,14 +1,13 @@
-{bionix, nixpkgs}:
+{bionix}:
 
-with nixpkgs;
 with bionix;
 
 rec {
-  jar = fetchurl {
+  jar = pkgs.fetchurl {
     url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar";
     sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k";
   };
-  gridssConfig = callBionixE ./gridss-configFile.nix {};
+  genConfig = callBionixE ./gridss-configFile.nix {};
   callVariants = callBionixE ./gridss-callVariants.nix;
   computeSamTags = callBionixE ./gridss-computeSamTags.nix;
   softClipsToSplitReads = callBionixE ./gridss-softClipsToSplitReads.nix;
diff --git a/tools/infercnv-infer.nix b/tools/infercnv-infer.nix
index 95ebbe3..0915691 100644
--- a/tools/infercnv-infer.nix
+++ b/tools/infercnv-infer.nix
@@ -1,15 +1,14 @@
 {bionix
-,nixpkgs
 ,flags ? null}:
 
-with nixpkgs;
+with bionix;
 with lib;
 
 {ref
 ,expr
 ,pos}:
 
-stdenv.mkDerivation {
+stage {
   name = "inferCNV";
   buildInputs = [ bionix.infercnv.app ];
   buildCommand = ''
diff --git a/tools/infercnv.nix b/tools/infercnv.nix
index 03e073b..71ed274 100644
--- a/tools/infercnv.nix
+++ b/tools/infercnv.nix
@@ -1,6 +1,5 @@
-{nixpkgs, bionix}:
+{bionix}:
 
-with nixpkgs;
 with bionix;
 
 {
diff --git a/tools/kallisto-index.nix b/tools/kallisto-index.nix
index 33dfb80..3b92d38 100644
--- a/tools/kallisto-index.nix
+++ b/tools/kallisto-index.nix
@@ -1,11 +1,10 @@
 {bionix
-, nixpkgs
 , kmerSize ? 31
 , unique ? false}:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 assert (kmerSize > 1);
 
@@ -13,9 +12,9 @@ input:
 
 assert (matchFiletype input { fa = _: true; } input);
 
-stdenv.mkDerivation {
+stage {
   name = "kallisto-index";
-  buildInputs = [ kallisto ];
+  buildInputs = with pkgs; [ kallisto ];
   buildCommand = ''
     kallisto index -k ${toString kmerSize} ${optionalString unique "--make-unique"} -i $out ${input}
   '';
diff --git a/tools/kallisto-quant.nix b/tools/kallisto-quant.nix
index c410721..1deab67 100644
--- a/tools/kallisto-quant.nix
+++ b/tools/kallisto-quant.nix
@@ -1,5 +1,4 @@
 {bionix
-, nixpkgs
 , indexFlags ? {}
 , bias ? false
 , bootstrapSamples ? 0
@@ -13,7 +12,7 @@
 , fragmentSD ? null
 , ref}:
 
-with nixpkgs;
+with bionix;
 with lib;
 
 assert (!single || (fragmentLength != null && fragmentSD != null));
@@ -27,9 +26,9 @@ in
 
 assert (all (x: isFastQ (x.filetype)) inputs);
 
-stdenv.mkDerivation {
+stage {
   name = "kallisto-quant";
-  buildInputs = [ kallisto ];
+  buildInputs = with pkgs; [ kallisto ];
   buildCommand = ''
     mkdir $out
     kallisto quant \
diff --git a/tools/kallisto.nix b/tools/kallisto.nix
index 8a5d038..31e15d9 100644
--- a/tools/kallisto.nix
+++ b/tools/kallisto.nix
@@ -1,4 +1,4 @@
-{bionix, nixpkgs}:
+{bionix}:
 
 with bionix;
 
diff --git a/tools/mosdepth-depth.nix b/tools/mosdepth-depth.nix
index 7043c43..448da11 100644
--- a/tools/mosdepth-depth.nix
+++ b/tools/mosdepth-depth.nix
@@ -1,17 +1,16 @@
 { bionix
-, nixpkgs
 , indexAttrs ? {}
 , flags ? null
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
 
 input:
 
-stdenv.mkDerivation {
+stage {
   name = "mosdepth-depth";
-  buildInputs = [ mosdepth ];
+  buildInputs = with pkgs; [ mosdepth ];
   buildCommand = ''
     mkdir $out
     ln -s ${input} input.bam
diff --git a/tools/mosdepth-plot.nix b/tools/mosdepth-plot.nix
index f15e099..0fdfc67 100644
--- a/tools/mosdepth-plot.nix
+++ b/tools/mosdepth-plot.nix
@@ -1,17 +1,16 @@
 { bionix
-, nixpkgs
 , flags ? null
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
 
 { inputs
 , names ? []}:
 
-stdenv.mkDerivation {
+stage {
   name = "mosdepth-depth";
-  buildInputs = [ python ];
+  buildInputs = with pkgs; [ python ];
   buildCommand = ''
     python ${mosdepth.src}/scripts/plot-dist.py ${concatMapStringsSep " " (i: "${i}/out.mosdepth.global.dist.txt") inputs}
     ${concatStringsSep "\n" (zipListsWith (i: n: "substituteInPlace dist.html --replace ${i}/out ${n}") inputs names)}
diff --git a/tools/mosdepth.nix b/tools/mosdepth.nix
index fa1101a..a5083a7 100644
--- a/tools/mosdepth.nix
+++ b/tools/mosdepth.nix
@@ -1,4 +1,4 @@
-{ bionix, nixpkgs }:
+{ bionix }:
 
 with bionix;
 
diff --git a/tools/mutect-call.nix b/tools/mutect-call.nix
index 9fd009b..e2fe3a1 100644
--- a/tools/mutect-call.nix
+++ b/tools/mutect-call.nix
@@ -1,13 +1,12 @@
 {bionix
-, nixpkgs
 , cosmic
 , dbsnp}:
 
-with nixpkgs;
+with bionix;
 with lib;
 
 let
-  inherit (bionix.types) matchFiletype;
+  inherit (types) matchFiletype;
   getVCFref = matchFiletype "mutect-call" {vcf = {ref}: ref;};
   getBAMref = matchFiletype "mutect-call" {bam = {ref, ...}: ref;};
   refs = map getVCFref [ cosmic dbsnp ];
@@ -20,7 +19,7 @@ assert (length (unique refs) == 1);
 
 assert (ref == getBAMref normal && ref == getBAMref tumour);
 
-stdenv.mkDerivation {
+stage {
   name = "mutect";
   buildInputs = [ bionix.mutect.app ];
   buildCommand = ''
diff --git a/tools/mutect.nix b/tools/mutect.nix
index 627b77e..59aff0a 100644
--- a/tools/mutect.nix
+++ b/tools/mutect.nix
@@ -1,9 +1,8 @@
-{bionix, nixpkgs}:
+{bionix}:
 
-with nixpkgs;
 with bionix;
 
 {
-  app = callPackage ./mutect-app.nix {inherit (nixpkgs) stdenv fetchurl makeWrapper unzip fetchFromGitHub;};
+  app = pkgs.callPackage ./mutect-app.nix {inherit (pkgs) stdenv fetchurl makeWrapper unzip fetchFromGitHub;};
   call = callBionixE ./mutect-call.nix;
 }
diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
index a57aa83..a5e497e 100644
--- a/tools/platypus-callVariants.nix
+++ b/tools/platypus-callVariants.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , indexAttrs ? {}
 , bamIndexAttrs ? {}
 , flags ? null
@@ -7,9 +6,9 @@
 
 inputs:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 
 let
@@ -21,9 +20,9 @@ in
 
 assert (length (unique refs) == 1);
 
-stdenv.mkDerivation {
+stage {
   name = "platypus";
-  buildInputs = [ platypus ];
+  buildInputs = with pkgs; [ platypus ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
diff --git a/tools/platypus.nix b/tools/platypus.nix
index 1b214dc..4379675 100644
--- a/