treewide reformatting and simplification

- simplify with statix
- reformat with nixpkgs-fmt

87 files changed, 521 insertions, 455 deletions

diff --git a/tools/ascat-app.nix b/tools/ascat-app.nix
index 51aa677..bd6d538 100644
--- a/tools/ascat-app.nix
+++ b/tools/ascat-app.nix
@@ -1,4 +1,4 @@
-{stdenv, callPackage, buildPerlPackage, fetchurl, fetchFromGitHub, perlPackages, R, bwa, samtools, pkgconfig, zlib, htslib, curl, bzip2, lzma, gnutls, nettle, gmp, p11-kit, libtasn1, perl, psmisc, time, vcftools, rWrapper, rPackages}:
+{ stdenv, callPackage, buildPerlPackage, fetchurl, fetchFromGitHub, perlPackages, R, bwa, samtools, pkgconfig, zlib, htslib, curl, bzip2, lzma, gnutls, nettle, gmp, p11-kit, libtasn1, perl, psmisc, time, vcftools, rWrapper, rPackages }:
 
 let
   ascat = fetchurl {
@@ -98,7 +98,7 @@ let
       url = "mirror://cpan/authors/id/C/CD/CDRAUG/${name}.tar.gz";
       sha256 = "0yvhgifs8g9rwdcq84zw4b005nq2jml6c75zgjscv6d2pd3lj1ss";
     };
-    propagatedBuildInputs = with perlPackages; [DBI DataStag Error GD Graph HTTPMessage HTTPMessage IOstringy IOString IPCRun LWP ListMoreUtils SetScalar TestMost TestRequiresInternet URI XMLDOM XMLDOMXPath XMLLibXML XMLLibXML libxml_perl XMLSAX XMLSAXBase XMLSAXWriter XMLTwig XMLWriter YAML DBFile ];
+    propagatedBuildInputs = with perlPackages; [ DBI DataStag Error GD Graph HTTPMessage HTTPMessage IOstringy IOString IPCRun LWP ListMoreUtils SetScalar TestMost TestRequiresInternet URI XMLDOM XMLDOMXPath XMLLibXML XMLLibXML libxml_perl XMLSAX XMLSAXBase XMLSAXWriter XMLTwig XMLWriter YAML DBFile ];
     nativeBuildInputs = with perlPackages; [ TestException TestWarn TestDifferences TestDeep ];
   };
 
@@ -108,7 +108,7 @@ let
       url = "mirror://cpan/authors/id/C/CM/CMUNGALL/${name}.tar.gz";
       sha256 = "0ncf4l39ka23nb01jlm6rzxdb5pqbip01x0m38bnvf1gim825caa";
     };
-    propagatedBuildInputs = with perlPackages; [IOString Graph XMLLibXSLT ];
+    propagatedBuildInputs = with perlPackages; [ IOString Graph XMLLibXSLT ];
   };
 
   XMLDOMXPath = buildPerlPackage rec {
@@ -117,7 +117,7 @@ let
       url = "mirror://cpan/authors/id/M/MI/MIROD/${name}.tar.gz";
       sha256 = "1si9m1pqih3ibbd6jnw69fh98dd4krxpx90p65x9j4aja55afwq1";
     };
-    propagatedBuildInputs= with perlPackages; [XMLDOM XMLXPathEngine];
+    propagatedBuildInputs = with perlPackages; [ XMLDOM XMLXPathEngine ];
     doCheck = false;
   };
 
@@ -215,10 +215,10 @@ let
     name = "alleleCount.pl-${version}";
     version = "4.0.1";
     src = fetchFromGitHub {
-    owner = "cancerit";
-    repo = "alleleCount";
-    rev = "v${version}";
-    sha256 = "0nkwnjqglgshzhlmz1r0khdjai9mfz4ih8bzrzg0g18d1725k6gp";
+      owner = "cancerit";
+      repo = "alleleCount";
+      rev = "v${version}";
+      sha256 = "0nkwnjqglgshzhlmz1r0khdjai9mfz4ih8bzrzg0g18d1725k6gp";
     };
     preConfigure = ''
       cd perl
@@ -266,4 +266,5 @@ let
     ];
   };
 
-in ascatNGS
+in
+ascatNGS
diff --git a/tools/ascat-callCNV.nix b/tools/ascat-callCNV.nix
index f74bb18..aa1a8ec 100644
--- a/tools/ascat-callCNV.nix
+++ b/tools/ascat-callCNV.nix
@@ -1,12 +1,12 @@
 { bionix
 , ref
 , gc
-, indexAttrs ? {}
-, bamIndexAttrs ? {}
+, indexAttrs ? { }
+, bamIndexAttrs ? { }
 , flags ? null
 }:
 
-{tumour, normal, gender}:
+{ tumour, normal, gender }:
 
 with bionix;
 with lib;
diff --git a/tools/ascat.nix b/tools/ascat.nix
index 700cb4e..142e0d9 100644
--- a/tools/ascat.nix
+++ b/tools/ascat.nix
@@ -1,17 +1,17 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
 {
-  app = pkgs.callPackage ./ascat-app.nix {};
+  app = pkgs.callPackage ./ascat-app.nix { };
 
   /* Generate GC correction file for ascatNGS.
-  Type: gccorrect :: {ref :: fasta, chrPrefix :: string, ...} -> (snps :: VCF) -> (gc :: GC)
+    Type: gccorrect :: {ref :: fasta, chrPrefix :: string, ...} -> (snps :: VCF) -> (gc :: GC)
   */
   gccorrect = callBionixE ./ascat-gccorrect.nix;
 
   /* Call CNVs using ascatNGS. Gender is a string as per ascatNGS docs (e.g., "XX").
-  Type: callCNV :: {ref :: fasta, gc :: GC, ...} -> {tumour :: bam, normal :: bam, gender :: string} -> CNVs
+    Type: callCNV :: {ref :: fasta, gc :: GC, ...} -> {tumour :: bam, normal :: bam, gender :: string} -> CNVs
   */
   callCNV = callBionixE ./ascat-callCNV.nix;
 }
diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix
index c83c49c..8df3dba 100644
--- a/tools/bowtie-align.nix
+++ b/tools/bowtie-align.nix
@@ -2,7 +2,7 @@
 , ref
 , bamOutput ? true
 , flags ? null
-, indexAttrs ? {}
+, indexAttrs ? { }
 }:
 
 { input1
@@ -18,7 +18,8 @@ let
   fa = f: matchFiletype "bowtie2-ref" { fa = _: f; } f;
   fq = f: matchFiletype "bowtie2-input" { fq = _: f; gz = matchFiletype' "bowtie2-input" { fq = _: f; }; } f;
 
-in stage {
+in
+stage {
   name = "bowtie2-align";
   buildInputs = with pkgs; [ bowtie2 bc samtools ];
   buildCommand = ''
@@ -32,6 +33,6 @@ in stage {
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
 }
diff --git a/tools/bowtie.nix b/tools/bowtie.nix
index df97d36..2208dff 100644
--- a/tools/bowtie.nix
+++ b/tools/bowtie.nix
@@ -4,12 +4,12 @@ with bionix;
 
 {
   /* Align a sequence against a reference
-  Type: align :: {ref :: fasta, bamOutput :: bool, ...} -> {input1 :: fastq, input2 :: fastq} -> bam/sam
+    Type: align :: {ref :: fasta, bamOutput :: bool, ...} -> {input1 :: fastq, input2 :: fastq} -> bam/sam
   */
   align = callBionixE ./bowtie-align.nix;
 
   /* Create a Bowtie index
-  Type: index :: {seed :: int, ...} -> fasta -> index
+    Type: index :: {seed :: int, ...} -> fasta -> index
   */
   index = callBionixE ./bowtie-index.nix;
 }
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 31c9487..52e73d1 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -2,7 +2,7 @@
 , ref
 , bamOutput ? true
 , flags ? null
-, indexAttrs ? {}
+, indexAttrs ? { }
 }:
 
 { input1
@@ -18,7 +18,8 @@ let
   fa = f: matchFiletype "bwa-ref" { fa = _: f; } f;
   fq = f: matchFiletype "bwa-input" { fq = _: f; gz = matchFiletype' "bwa-input" { fq = _: f; }; } f;
 
-in stage {
+in
+stage {
   name = "bwa-mem";
   buildInputs = with pkgs; [ bwa bc ] ++ optional bamOutput samtools;
   buildCommand = ''
@@ -35,6 +36,6 @@ in stage {
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
 }
diff --git a/tools/bwa-mem2-app.nix b/tools/bwa-mem2-app.nix
index 49f4af3..6ee2ab4 100644
--- a/tools/bwa-mem2-app.nix
+++ b/tools/bwa-mem2-app.nix
@@ -1,5 +1,5 @@
 { clangStdenv, fetchFromGitHub, zlib }:
-  clangStdenv.mkDerivation rec {
+clangStdenv.mkDerivation rec {
   pname = "bwa-mem2";
   version = "2.1";
   src = fetchFromGitHub {
diff --git a/tools/bwa-mem2.nix b/tools/bwa-mem2.nix
index b16b7ea..843c5b0 100644
--- a/tools/bwa-mem2.nix
+++ b/tools/bwa-mem2.nix
@@ -2,7 +2,7 @@
 , ref
 , bamOutput ? true
 , flags ? null
-, indexAttrs ? {}
+, indexAttrs ? { }
 }:
 
 { input1
@@ -18,7 +18,8 @@ let
   fa = f: matchFiletype "bwa-ref" { fa = _: f; } f;
   fq = f: matchFiletype "bwa-input" { fq = _: f; gz = matchFiletype' "bwa-input" { fq = _: f; }; } f;
 
-in stage {
+in
+stage {
   name = "bwa-mem2";
   buildInputs = with pkgs; [ bionix.bwa.app2 bc ] ++ optional bamOutput samtools;
   buildCommand = ''
@@ -35,6 +36,6 @@ in stage {
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
 }
diff --git a/tools/bwa.nix b/tools/bwa.nix
index 90a8bd3..6fb7d71 100644
--- a/tools/bwa.nix
+++ b/tools/bwa.nix
@@ -3,18 +3,18 @@
 with bionix;
 
 rec {
-  app2 = pkgs.callPackage ./bwa-mem2-app.nix {};
+  app2 = pkgs.callPackage ./bwa-mem2-app.nix { };
 
   /* Align read against a reference: defaults to bwa-mem */
   align = bionix.bwa.mem;
 
   /* Align reads against a reference using bwa-mem
-  Type: bwa-mem :: {ref :: fasta, bamOutput :: bool, ...} -> {input1, input2} -> bam/sam
+    Type: bwa-mem :: {ref :: fasta, bamOutput :: bool, ...} -> {input1, input2} -> bam/sam
   */
   mem = callBionixE ./bwa-mem.nix;
   mem2 = callBionixE ./bwa-mem2.nix;
   /* Creates an reference index for BWA
-  Type: index :: {...} -> fasta -> BWA index
+    Type: index :: {...} -> fasta -> BWA index
   */
   index = callBionixE ./bwa-index.nix;
   index2 = callBionixE ./bwa-index2.nix;
diff --git a/tools/cnvkit-batch.nix b/tools/cnvkit-batch.nix
index 113e0c9..7f7893f 100644
--- a/tools/cnvkit-batch.nix
+++ b/tools/cnvkit-batch.nix
@@ -1,17 +1,18 @@
-{bionix
-,targets ? null
-,annotations ? null
-,flags ? null
-,indexAttrs ? {}}:
+{ bionix
+, targets ? null
+, annotations ? null
+, flags ? null
+, indexAttrs ? { }
+}:
 
-{normals ? [], tumours}:
+{ normals ? [ ], tumours }:
 
 with bionix;
 with lib;
 with types;
 
 let
-  getref = f: matchFiletype "cnvkit-batch" { bam = {ref, ...}: ref; } f;
+  getref = matchFiletype "cnvkit-batch" { bam = { ref, ... }: ref; };
   refs = map getref normals ++ map getref tumours;
   ref = head refs;
   sorted = matchFileSorting "cnvkit-batch" { coord = _: true; };
diff --git a/tools/cnvkit-scatter.nix b/tools/cnvkit-scatter.nix
index 2899584..6cd5b96 100644
--- a/tools/cnvkit-scatter.nix
+++ b/tools/cnvkit-scatter.nix
@@ -1,5 +1,6 @@
-{bionix
-,flags ? null}:
+{ bionix
+, flags ? null
+}:
 
 input:
 
diff --git a/tools/cnvkit.nix b/tools/cnvkit.nix
index fc55d94..812652a 100644
--- a/tools/cnvkit.nix
+++ b/tools/cnvkit.nix
@@ -1,15 +1,15 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
 {
   /* Call CNVs
-  Type: callCNV :: {targets :: target file, annotations :: annotation file, ...} -> {normals :: [bam], tumours :: [bam]} -> CNVs
+    Type: callCNV :: {targets :: target file, annotations :: annotation file, ...} -> {normals :: [bam], tumours :: [bam]} -> CNVs
   */
   callCNV = callBionixE ./cnvkit-batch.nix;
 
   /* Scatter plot from CNV calls
-  Type: scatterPlot :: {} -> CNVs -> PDF
+    Type: scatterPlot :: {} -> CNVs -> PDF
   */
   scatterPlot = callBionixE ./cnvkit-scatter.nix;
 }
diff --git a/tools/compression-bunzip2.nix b/tools/compression-bunzip2.nix
index 06fe682..a36b66d 100644
--- a/tools/compression-bunzip2.nix
+++ b/tools/compression-bunzip2.nix
@@ -1,4 +1,4 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
diff --git a/tools/compression-bzip2.nix b/tools/compression-bzip2.nix
index 6dfb749..5332e7d 100644
--- a/tools/compression-bzip2.nix
+++ b/tools/compression-bzip2.nix
@@ -1,4 +1,4 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
diff --git a/tools/compression-gunzip.nix b/tools/compression-gunzip.nix
index 6c98f91..96a4e49 100644
--- a/tools/compression-gunzip.nix
+++ b/tools/compression-gunzip.nix
@@ -1,4 +1,4 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
diff --git a/tools/compression-gzip.nix b/tools/compression-gzip.nix
index 50fca9e..0229b94 100644
--- a/tools/compression-gzip.nix
+++ b/tools/compression-gzip.nix
@@ -1,4 +1,4 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
diff --git a/tools/compression.nix b/tools/compression.nix
index bfcc292..c9c8777 100644
--- a/tools/compression.nix
+++ b/tools/compression.nix
@@ -1,4 +1,4 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 with types;
@@ -8,42 +8,51 @@ let
   gunzip = callBionixE ./compression-gunzip.nix;
   bunzip2 = callBionixE ./compression-bunzip2.nix;
 
-in {
-  uncompress = attrs: f: matchFiletype "uncompress" {
-    fa = _: f;
-    fq = _: f;
-    bam = _: f;
-    sam = _: f;
-    cram = _: f;
-    vcf = _: f;
-    bed = _: f;
-    gz = _: gunzip attrs f;
-    bz2 = _: bunzip2 attrs f;
-  } f;
+in
+{
+  uncompress = attrs: f: matchFiletype "uncompress"
+    {
+      fa = _: f;
+      fq = _: f;
+      bam = _: f;
+      sam = _: f;
+      cram = _: f;
+      vcf = _: f;
+      bed = _: f;
+      gz = _: gunzip attrs f;
+      bz2 = _: bunzip2 attrs f;
+    }
+    f;
 
   gzip = attrs: f:
     let gz = gzip attrs f;
-    in types.matchFiletype "compressed" {
-      fa = _: gz;
-      fq = _: gz;
-      bam = _: gz;
-      sam = _: gz;
-      cram = _: gz;
-      vcf = _: gz;
-      bed = _: gz;
-      gz = x: x;
-    } f;
+    in
+    types.matchFiletype "compressed"
+      {
+        fa = _: gz;
+        fq = _: gz;
+        bam = _: gz;
+        sam = _: gz;
+        cram = _: gz;
+        vcf = _: gz;
+        bed = _: gz;
+        gz = x: x;
+      }
+      f;
 
   bzip2 = attrs: f:
     let bz2 = bzip2 attrs f;
-    in types.matchFiletype "compressed" {
-      fa = _: gz;
-      fq = _: gz;
-      bam = _: gz;
-      sam = _: gz;
-      cram = _: gz;
-      vcf = _: gz;
-      bed = _: gz;
-      bz2 = x: x;
-    } f;
+    in
+    types.matchFiletype "compressed"
+      {
+        fa = _: gz;
+        fq = _: gz;
+        bam = _: gz;
+        sam = _: gz;
+        cram = _: gz;
+        vcf = _: gz;
+        bed = _: gz;
+        bz2 = x: x;
+      }
+      f;
 }
diff --git a/tools/crumble-app.nix b/tools/crumble-app.nix
index fc30d5a..d8ed1a7 100644
--- a/tools/crumble-app.nix
+++ b/tools/crumble-app.nix
@@ -1,4 +1,4 @@
-{stdenv, fetchFromGitHub, autoreconfHook, htslib}:
+{ stdenv, fetchFromGitHub, autoreconfHook, htslib }:
 
 stdenv.mkDerivation rec {
   name = "crumble-${version}";
diff --git a/tools/crumble.nix b/tools/crumble.nix
index 4256f37..dfb4e31 100644
--- a/tools/crumble.nix
+++ b/tools/crumble.nix
@@ -3,5 +3,5 @@
 with bionix;
 
 {
-  crumble = pkgs.callPackage ./crumble-app.nix {};
+  crumble = pkgs.callPackage ./crumble-app.nix { };
 }
diff --git a/tools/delly-call.nix b/tools/delly-call.nix
index 5378810..80084be 100644
--- a/tools/delly-call.nix
+++ b/tools/delly-call.nix
@@ -1,4 +1,4 @@
-{ bionix, flags ? "", faidxAttrs ? {}, indexAttrs ? {}}:
+{ bionix, flags ? "", faidxAttrs ? { }, indexAttrs ? { } }:
 
 inputs:
 
@@ -41,6 +41,6 @@ stage {
   '';
   passthru = {
     multicore = true;
-    filetype = filetype.vcf { ref = ref; };
+    filetype = filetype.vcf { inherit ref; };
   };
 }
diff --git a/tools/delly.nix b/tools/delly.nix
index d94457c..22d4d89 100644
--- a/tools/delly.nix
+++ b/tools/delly.nix
@@ -4,7 +4,7 @@ with bionix;
 
 {
   /* Call structural variants
-  Type: call { ... } -> [bam] -> vcf
+    Type: call { ... } -> [bam] -> vcf
   */
   call = callBionixE ./delly-call.nix;
 }
diff --git a/tools/facets-app.nix b/tools/facets-app.nix
index 6553a67..fe2a31b 100644
--- a/tools/facets-app.nix
+++ b/tools/facets-app.nix
@@ -1,8 +1,9 @@
-{buildRPackage
-,fetchFromGitHub
-,R
-,htslib
-,zlib}:
+{ buildRPackage
+, fetchFromGitHub
+, R
+, htslib
+, zlib
+}:
 
 let
   pctGCdata = buildRPackage rec {
@@ -18,7 +19,8 @@ let
     buildInputs = [ R ];
   };
 
-in buildRPackage rec{
+in
+buildRPackage rec{
   name = "facets-${version}";
   version = "0.6.1";
   requireX = false;
diff --git a/tools/facets-call.nix b/tools/facets-call.nix
index a736627..43c4c7f 100644
--- a/tools/facets-call.nix
+++ b/tools/facets-call.nix
@@ -1,6 +1,6 @@
-{bionix}:
+{ bionix }:
 
-{vcf, bams}:
+{ vcf, bams }:
 
 with bionix;
 with types;
diff --git a/tools/facets.nix b/tools/facets.nix
index 14110a9..b91e422 100644
--- a/tools/facets.nix
+++ b/tools/facets.nix
@@ -1,12 +1,12 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
 {
-  app = lib.callPackageWith (pkgs // pkgs.rPackages) ./facets-app.nix {};
+  app = lib.callPackageWith (pkgs // pkgs.rPackages) ./facets-app.nix { };
 
   /* Call CNVs
-  Type: callCnv :: {...} -> {vcf, bams :: [bams]} -> CNVs
+    Type: callCnv :: {...} -> {vcf, bams :: [bams]} -> CNVs
   */
   callCNV = callBionixE ./facets-call.nix;
 }
diff --git a/tools/fastp-check.nix b/tools/fastp-check.nix
index 06f00ae..9467cd9 100644
--- a/tools/fastp-check.nix
+++ b/tools/fastp-check.nix
@@ -1,10 +1,10 @@
 { bionix
 , flags ? null
-} :
+}:
 
 { input1
 , input2 ? null
-} :
+}:
 
 with bionix;
 with lib;
@@ -15,26 +15,27 @@ let
 
   out =
     stage {
-        name = "fastp";
-        buildInputs = [ pkgs.fastp ];
-        outputs = [ "out" "fastq1" "json" ] ++ (if input2 != null then [ "fastq2" ] else []);
-        buildCommand = ''
-            mkdir -p $out
-            fastp \
-                ${optionalString (flags != null) flags} \
-                -i ${fq input1} \
-                -o fastq1.fq.gz \
-                ${optionalString (input2 != null) ''
-                    -I ${fq input2} \
-                    -O fastq2.fq.gz \
+      name = "fastp";
+      buildInputs = [ pkgs.fastp ];
+      outputs = [ "out" "fastq1" "json" ] ++ (if input2 != null then [ "fastq2" ] else [ ]);
+      buildCommand = ''
+        mkdir -p $out
+        fastp \
+            ${optionalString (flags != null) flags} \
+            -i ${fq input1} \
+            -o fastq1.fq.gz \
+            ${optionalString (input2 != null) ''
+                -I ${fq input2} \
+                -O fastq2.fq.gz \
 
-                    cp fastq2.fq.gz $fastq2
-                ''}
+                cp fastq2.fq.gz $fastq2
+            ''}
 
-                cp fastq1.fq.gz $fastq1
-                cp fastp.html $out
-                cp fastp.json $json
-        '';
+            cp fastq1.fq.gz $fastq1
+            cp fastp.html $out
+            cp fastp.json $json
+      '';
     };
-  fqgz = { filetype = filetype.gz (filetype.fastq {}); };
-in out // { fastq1 = out.fastq1 // fqgz; } // (if input2 != null then {fastq2 = out.fastq2 // fqgz; } else {})
+  fqgz = { filetype = filetype.gz (filetype.fastq { }); };
+in
+out // { fastq1 = out.fastq1 // fqgz; } // (if input2 != null then { fastq2 = out.fastq2 // fqgz; } else { })
diff --git a/tools/fastp.nix b/tools/fastp.nix
index 36bc690..454d100 100644
--- a/tools/fastp.nix
+++ b/tools/fastp.nix
@@ -3,9 +3,9 @@
 with bionix;
 
 rec {
-    /* Check and filter fastqs
+  /* Check and filter fastqs
     Type: { ... } -> { input1, input2 ? null } -> { out :: html, fastq1 :: fastq, fastq2 :: fastq, json :: JSON } 
-    */
-    check = callBionixE ./fastp-check.nix;
+  */
+  check = callBionixE ./fastp-check.nix;
 }
 
diff --git a/tools/fastqc.nix b/tools/fastqc.nix
index 6279682..8c448b9 100644
--- a/tools/fastqc.nix
+++ b/tools/fastqc.nix
@@ -3,10 +3,10 @@
 with bionix;
 
 {
-  fastqc = pkgs.callPackage ./fastqc-app.nix {};
+  fastqc = pkgs.callPackage ./fastqc-app.nix { };
 
   /* QC check
-  Type: check :: {...} -> input :: fastq -> report
+    Type: check :: {...} -> input :: fastq -> report
   */
   check = callBionixE ./fastqc-check.nix;
 }
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index 1a46eae..15e5ca6 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -1,12 +1,12 @@
 { bionix
-, bwaIndexAttrs ? {}
-, faidxAttrs ? {}
-, indexAttrs ? {}
-, collectMetricsAttrs ? {}
+, bwaIndexAttrs ? { }
+, faidxAttrs ? { }
+, indexAttrs ? { }
+, collectMetricsAttrs ? { }
 , flags ? null
 , config ? null
 , heapSize ? "31g"
-, workdirs ? []
+, workdirs ? [ ]
 , jobIndex ? null
 , jobNodes ? null
 }:
@@ -36,7 +36,7 @@ let
 in
 
 assert (all sorted inputs);
-assert (homoRef);
+assert homoRef;
 
 stage rec {
   name = "gridss-assemble";
@@ -70,6 +70,6 @@ stage rec {
     touch $out
     cp -r out.gridss.working $work
   '';
-  passthru.filetype = filetype.bam { ref = ref; sorting = sort.none {}; };
+  passthru.filetype = filetype.bam { inherit ref; sorting = sort.none { }; };
   passthru.multicore = true;
 }
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index f42e3f3..ad659de 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -1,7 +1,7 @@
 { bionix
 , blacklist ? null
-, bwaIndexAttrs ? {}
-, faidxAttrs ? {}
+, bwaIndexAttrs ? { }
+, faidxAttrs ? { }
 , flags ? null
 , config ? null
 , heapSize ? "31g"
@@ -32,22 +32,22 @@ stage rec {
     done
     mkdir $out
     java -ea -Xmx${heapSize} \
-	    -Dreference_fasta="ref.fa" \
-	    -Dsamjdk.create_index=true \
-	    -Dsamjdk.use_async_io_read_samtools=true \
-	    -Dsamjdk.use_async_io_write_samtools=true \
-	    -Dsamjdk.use_async_io_write_tribble=true \
-	    -Dgridss.gridss.output_to_temp_file=true \
-	    -cp ${bionix.gridss.jar} gridss.CallVariants \
+      -Dreference_fasta="ref.fa" \
+      -Dsamjdk.create_index=true \
+      -Dsamjdk.use_async_io_read_samtools=true \
+      -Dsamjdk.use_async_io_write_samtools=true \
+      -Dsamjdk.use_async_io_write_tribble=true \
+      -Dgridss.gridss.output_to_temp_file=true \
+      -cp ${bionix.gridss.jar} gridss.CallVariants \
       VERBOSITY=WARNING \
       WORKER_THREADS=$NIX_BUILD_CORES \
-	    TMP_DIR=. \
-	    WORKING_DIR=. \
+      TMP_DIR=. \
+      WORKING_DIR=. \
       ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
-	    REFERENCE_SEQUENCE="ref.fa" \
+      REFERENCE_SEQUENCE="ref.fa" \
       ${concatMapStringsSep " " (i: "INPUT=\"${i}\"") inputs} \
-	    OUTPUT="$out/gridss.vcf" \
-	    ASSEMBLY="$out/gridss.bam" \
+      OUTPUT="$out/gridss.vcf" \
+      ASSEMBLY="$out/gridss.bam" \
       ${optionalString (blacklist != null) ("BLACKLIST=" + blacklist)} \
       ${optionalString (flags != null) flags}
 
diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix
index de44478..e07f6a5 100644
--- a/tools/gridss-computeSamTags.nix
+++ b/tools/gridss-computeSamTags.nix
@@ -1,5 +1,10 @@
-{ bionix, bwaIndexAttrs ? { }, faidxAttrs ? { }, flags ? null, config ? null
-, heapSize ? "1G" }:
+{ bionix
+, bwaIndexAttrs ? { }
+, faidxAttrs ? { }
+, flags ? null
+, config ? null
+, heapSize ? "1G"
+}:
 
 with bionix;
 with lib;
@@ -11,7 +16,8 @@ let
   ref = matchFiletype "gridss-computeSamTags" { bam = x: x.ref; } input;
   sorted = matchFileSorting "gridss-computeSamTags" { name = _: true; } input;
 
-in assert (sorted);
+in
+assert sorted;
 
 stage rec {
   name = "gridss-computeSamTags";
diff --git a/tools/gridss-configFile.nix b/tools/gridss-configFile.nix
index d6b600e..3d0d3f8 100644
--- a/tools/gridss-configFile.nix
+++ b/tools/gridss-configFile.nix
@@ -1,37 +1,41 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 with lib;
 
 let
-    attrsToGridssConfigString = attrsToGridssConfigStringPrepend "";
+  attrsToGridssConfigString = attrsToGridssConfigStringPrepend "";
 
-    attrsToGridssConfigStringPrepend = prepend: attrs:
-        concatStringsSep "\n" (
-            attrValues (
-                mapAttrs
-                    (name: attr: prepend + (iniLine name attr))
-                    attrs));
+  attrsToGridssConfigStringPrepend = prepend: attrs:
+    concatStringsSep "\n" (
+      attrValues (
+        mapAttrs
+          (name: attr: prepend + (iniLine name attr))
+          attrs));
 
-    iniLine = name: attr:
-        let attrType = builtins.typeOf attr;
-        in
-            if (iniLineByAttrType ? ${attrType})
-            then (iniLineByAttrType.${attrType} name attr)
-            else builtins.throw (
-               "`gridssConfig` cannot convert attribute of type \"" + attrType + "\".");
+  iniLine = name: attr:
+    let attrType = builtins.typeOf attr;
+    in
+    if (iniLineByAttrType ? "${attrType}")
+    then (iniLineByAttrType."${attrType}" name attr)
+    else
+      builtins.throw (
+        "`gridssConfig` cannot convert attribute of type \"" + attrType + "\"."
+      );
 
-    iniLineByAttrType = {
-        string = name: attr: name + " = " + attr;
-        int    = name: attr: name + " = " + builtins.toString attr;
-        float  = name: attr: name + " = " + (
-                    builtins.head (
-                        builtins.match "([0-9]+\.0?[1-9]*)0+" (builtins.toString attr)));
-        bool   = name: attr: name + " = " + (if attr == true then "true" else "false");
-        set    = name: attr: attrsToGridssConfigStringPrepend (name + ".") attr;
-        # Allows for repeated fields (e.g. for adapters):
-        list   = name: attr: concatStringsSep "\n" (map (x: iniLine name x) attr);
-    };
-in configAttrs: (pkgs.writeText
-        "gridss.properties.override"
-        ((attrsToGridssConfigString configAttrs) + "\n"))
+  iniLineByAttrType = {
+    string = name: attr: name + " = " + attr;
+    int = name: attr: name + " = " + builtins.toString attr;
+    float = name: attr: name + " = " + (
+      builtins.head (
+        builtins.match "([0-9]+\.0?[1-9]*)0+" (builtins.toString attr)
+      ));
+    bool = name: attr: name + " = " + (if attr then "true" else "false");
+    set = name: attrsToGridssConfigStringPrepend (name + ".");
+    # Allows for repeated fields (e.g. for adapters):
+    list = name: attr: concatStringsSep "\n" (map (iniLine name) attr);
+  };
+in
+configAttrs: (pkgs.writeText
+  "gridss.properties.override"
+  ((attrsToGridssConfigString configAttrs) + "\n"))
diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
index 6691808..ea268cf 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -1,10 +1,10 @@
 { bionix
-, dictIndexAttrs ? {}
-, faidxAttrs ? {}
+, dictIndexAttrs ? { }
+, faidxAttrs ? { }
 , flags ? null
 , unmappedReads ? false
 , minClipLength ? 5
-, collectMetricsAttrs ? {}
+, collectMetricsAttrs ? { }
 , config ? null
 }:
 
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 93d02df..ef53322 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -1,6 +1,6 @@
 { bionix
-, bwaIndexAttrs ? {}
-, faidxAttrs ? {}
+, bwaIndexAttrs ? { }
+, faidxAttrs ? { }
 , alignerStreaming ? false
 , flags ? null
 , config ? null
@@ -37,7 +37,7 @@ stage rec {
       ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
       WORKER_THREADS=$NIX_BUILD_CORES \
       ${optionalString (flags != null) flags}
-    '';
-  passthru.filetype = filetype.bam { ref = ref; sorting = sort.none {}; };
+  '';
+  passthru.filetype = filetype.bam { inherit ref; sorting = sort.none { }; };
   passthru.multicore = true;
 }
diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix
index a5c470a..62a89f6 100644
--- a/tools/gridss-variants.nix
+++ b/tools/gridss-variants.nix
@@ -1,7 +1,14 @@
-{ bionix, bwaIndexAttrs ? { }, faidxAttrs ? { }, indexAttrs ? { }
-, assemblyAttrs ? { }, collectMetricsAttrs ? { }
+{ bionix
+, bwaIndexAttrs ? { }
+, faidxAttrs ? { }
+, indexAttrs ? { }
+, assemblyAttrs ? { }
+, collectMetricsAttrs ? { }
 , softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; }
-, config ? null, heapSize ? "4g", shards ? 10 }:
+, config ? null
+, heapSize ? "4g"
+, shards ? 10
+}:
 
 with bionix;
 with lib;
@@ -47,15 +54,16 @@ let
     for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
       ln -s $f
     done
-    ${concatMapStringsSep "\n" (linkSV) inputs}
+    ${concatMapStringsSep "\n" linkSV inputs}
     ${linkSV assembly}
     ${concatMapStringsSep "\n" (linkInput collectMetrics collectMetricsAttrs)
     inputs}
     ${linkInput collectMetrics collectMetricsAttrs assembly}
   '';
 
-in assert (all sorted inputs);
-assert (homoRef);
+in
+assert (all sorted inputs);
+assert homoRef;
 
 rec {
   identify = stage rec {
@@ -80,7 +88,7 @@ rec {
       mv out.vcf $out
     '';
     passthru = {
-      filetype = filetype.vcf { ref = ref; };
+      filetype = filetype.vcf { inherit ref; };
       gridss.assembly = assembly;
       multicore = true;
     };
@@ -115,7 +123,7 @@ rec {
       mv out.vcf $out
     '';
     passthru = {
-      filetype = filetype.vcf { ref = ref; };
+      filetype = filetype.vcf { inherit ref; };
       gridss.assembly = assembly;
       multicore = true;
     };
diff --git a/tools/gridss.nix b/tools/gridss.nix
index 7372864..db577ad 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -10,60 +10,65 @@ rec {
   };
 
   /* Generate configuration file for GRIDSS. Takes attribute sets to GRIDSS ini style format.
-     Type: genConfig :: attrSet -> ini file
+    Type: genConfig :: attrSet -> ini file
   */
   genConfig = callBionix ./gridss-configFile.nix { };
 
   /* Invoke the callVariants tool
-     Type: callVariants :: {blacklist :: drv = null, config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> variants
+    Type: callVariants :: {blacklist :: drv = null, config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> variants
   */
   callVariants = callBionixE ./gridss-callVariants.nix;
 
   /* Invoke computeSamTags tool
-     Type: computeSamTags :: {config :: ini = null, heapSize :: String = "1G", ...} -> bam -> bam
+    Type: computeSamTags :: {config :: ini = null, heapSize :: String = "1G", ...} -> bam -> bam
   */
   computeSamTags = callBionixE ./gridss-computeSamTags.nix;
 
   /* Invoke softClipsToSplitReads tool
-     Type: softClipsToSplitReads :: {alignerStreaming :: Bool = false, config :: ini = null, heapSize :: String = "2G", ...} -> bam -> bam
+    Type: softClipsToSplitReads :: {alignerStreaming :: Bool = false, config :: ini = null, heapSize :: String = "2G", ...} -> bam -> bam
   */
   softClipsToSplitReads = callBionixE ./gridss-softClipsToSplitReads.nix;
 
   /* Invoke collectMetrics tool
-     Type: collectMetrics :: {thresholdCoverage :: Int = 10000, config :: ini = null, heapSize :: String = "1G", ...} -> bam -> metrics
+    Type: collectMetrics :: {thresholdCoverage :: Int = 10000, config :: ini = null, heapSize :: String = "1G", ...} -> bam -> metrics
   */
   collectMetrics = callBionixE ./gridss-collectMetrics.nix;
 
   /* Invoke extractSVReads tool
-     Type: extractSVReads :: {unmappedReads :: Bool = false, minClipLength :: Int = 5, config :: ini = null, ...} -> bam -> bam
+    Type: extractSVReads :: {unmappedReads :: Bool = false, minClipLength :: Int = 5, config :: ini = null, ...} -> bam -> bam
   */
   extractSVReads = callBionixE ./gridss-extractSVReads.nix;
 
   /* Invoke assembly tool
-     Type: assemble :: {config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> bam
+    Type: assemble :: {config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> bam
   */
   assemble = callBionixE ./gridss-assemble.nix;
   shardedAssemble = n: a: input:
     let
-      assemblies = genList (i:
-        bionix.gridss.assemble (a // {
-          jobNodes = n;
-          jobIndex = i;
-        }) input) n;
-    in if n <= 1 then
+      assemblies = genList
+        (i:
+          bionix.gridss.assemble
+            (a // {
+              jobNodes = n;
+              jobIndex = i;
+            })
+            input)
+        n;
+    in
+    if n <= 1 then
       bionix.gridss.assemble a input
     else
       bionix.gridss.assemble (a // { workdirs = map (a: a.work) assemblies; })
-      input;
+        input;
 
   /* Invoke identifyVariants tool
-     Type: identifyVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF
+    Type: identifyVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF
   */
   identifyVariants = exec
     (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify);
 
   /* Invoke annotateVariants tool
-     Type: annotateVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF
+    Type: annotateVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF
   */
   annotateVariants = exec
     (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate);
@@ -73,7 +78,7 @@ rec {
     ((callBionix ./gridss-variants.nix attrs) input).annotateAndAssemble);
 
   /* Preprocess BAM files to extract SV reads
-     Type: preprocessBam :: bam -> bam
+    Type: preprocessBam :: bam -> bam
   */
   preprocessBam = with samtools;
     flip pipe [
@@ -84,7 +89,7 @@ rec {
     ];
 
   /* Call SVs: entire pipeline including preprocessing. It is recommended to use this function rather than the individual above tools.
-     Type: [bam] -> GRIDSS result
+    Type: [bam] -> GRIDSS result
   */
   call = inputs: gridss.annotateVariants { } (map gridss.preprocessBam inputs);
 
diff --git a/tools/hisat2-align.nix b/tools/hisat2-align.nix
index 7a216a6..0a1eb25 100644
--- a/tools/hisat2-align.nix
+++ b/tools/hisat2-align.nix
@@ -2,7 +2,7 @@
 , ref
 , bamOutput ? true
 , flags ? null
-, indexAttrs ? {}
+, indexAttrs ? { }
 }:
 
 { input1
@@ -18,7 +18,8 @@ let
   fa = f: matchFiletype "hisat2-ref" { fa = _: f; } f;
   fq = f: matchFiletype "hisat2-input" { fq = _: f; gz = matchFiletype' "hisat2-input" { fq = _: "<(gunzip < ${f})"; }; } f;
 
-in stage {
+in
+stage {
   name = "hisat2-align";
   buildInputs = with pkgs; [ hisat2 bc samtools ];
   buildCommand = ''
@@ -33,6 +34,6 @@ in stage {
       | samtools sort -n \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
 }
diff --git a/tools/hisat2-index.nix b/tools/hisat2-index.nix
index ffdb4ed..d9d5cd1 100644
--- a/tools/hisat2-index.nix
+++ b/tools/hisat2-index.nix
@@ -1,8 +1,8 @@
 { bionix
 , gtf ? null
 , flags ? null
-, extractSpliceSitesAttrs ? {}
-, extractExonsAttrs ? {}
+, extractSpliceSitesAttrs ? { }
+, extractExonsAttrs ? { }
 }:
 
 ref:
diff --git a/tools/hisat2.nix b/tools/hisat2.nix
index 8cc4ddf..e3e9995 100644
--- a/tools/hisat2.nix
+++ b/tools/hisat2.nix
@@ -4,12 +4,12 @@ with bionix;
 
 rec {
   /* Align read against a reference
-  Type: hisat2-mem :: {ref :: fasta, bamOutput :: bool, ...} -> {input1, input2} -> bam/sam
+    Type: hisat2-mem :: {ref :: fasta, bamOutput :: bool, ...} -> {input1, input2} -> bam/sam
   */
   align = callBionixE ./hisat2-align.nix;
 
   /* Creates an reference index for HISAT2
-  Type: index :: {...} -> fasta -> HISAT2 index
+    Type: index :: {...} -> fasta -> HISAT2 index
   */
   index = callBionixE ./hisat2-index.nix;
 
diff --git a/tools/infercnv-app.nix b/tools/infercnv-app.nix
index 5114e2f..36b9956 100644
--- a/tools/infercnv-app.nix
+++ b/tools/infercnv-app.nix
@@ -1,21 +1,22 @@
-{stdenv
-  ,fetchurl
-  ,fetchFromGitHub
-  ,callPackage
-  ,nettools
-  ,rPackages
-  ,rWrapper
-  ,R
-  ,jre
-  ,python
-  ,pythonPackages
-  ,darwin
-  ,gettext
-  ,gfortran
-,makeWrapper}:
+{ stdenv
+, fetchurl
+, fetchFromGitHub
+, callPackage
+, nettools
+, rPackages
+, rWrapper
+, R
+, jre
+, python
+, pythonPackages
+, darwin
+, gettext
+, gfortran
+, makeWrapper
+}:
 
 let
-  buildRPackage = rPackages.buildRPackage;
+  inherit (rPackages) buildRPackage;
 
   GMD = buildRPackage rec {
     name = "GMD-${version}";
@@ -59,7 +60,7 @@ let
       owner = "broadinstitute";
       repo = "inferCNV";
       rev = "cf442af0db6191fa8ba57c4921ac2d1f98c2c39d";
-        sha256 = "0cv8qiaqpd6b4152dplnzvgv77cmk961rmvzr27qgmlaazc5hblh";
+      sha256 = "0cv8qiaqpd6b4152dplnzvgv77cmk961rmvzr27qgmlaazc5hblh";
     };
     propagatedBuildInputs = with rPackages; [ R GMD NGCHMR RColorBrewer gplots optparse logging ];
   };
@@ -75,9 +76,10 @@ let
     sha256 = "1pz710ig8nnydz329ry8fydccbrp3arp614dgba3bcyy9flm3gnw";
   };
 
-in stdenv.mkDerivation rec {
-  name = inferCNV.name;
-  src = inferCNV.src;
+in
+stdenv.mkDerivation rec {
+  inherit (inferCNV) name;
+  inherit (inferCNV) src;
   buildInputs = [ r makeWrapper py ];
   propagatedBuildInputs = [ jre ];
   installPhase = ''
diff --git a/tools/infercnv-infer.nix b/tools/infercnv-infer.nix
index 0915691..e499f6c 100644
--- a/tools/infercnv-infer.nix
+++ b/tools/infercnv-infer.nix
@@ -1,12 +1,14 @@
-{bionix
-,flags ? null}:
+{ bionix
+, flags ? null
+}:
 
 with bionix;
 with lib;
 
-{ref
-,expr
-,pos}:
+{ ref
+, expr
+, pos
+}:
 
 stage {
   name = "inferCNV";
diff --git a/tools/infercnv.nix b/tools/infercnv.nix
index 71ed274..86ffb74 100644
--- a/tools/infercnv.nix
+++ b/tools/infercnv.nix
@@ -1,8 +1,8 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
 {
-  app = callPackage ./infercnv-app.nix {};
-  infercnv = callBionixE ./infercnv-infer.nix {};
+  app = callPackage ./infercnv-app.nix { };
+  infercnv = callBionixE ./infercnv-infer.nix { };
 }
diff --git a/tools/kallisto-index.nix b/tools/kallisto-index.nix
index 3b92d38..074a953 100644
--- a/tools/kallisto-index.nix
+++ b/tools/kallisto-index.nix
@@ -1,6 +1,7 @@
-{bionix
+{ bionix
 , kmerSize ? 31
-, unique ? false}:
+, unique ? false
+}:
 
 with bionix;
 with lib;
diff --git a/tools/kallisto-quant.nix b/tools/kallisto-quant.nix
index 3efeaaa..b7481d8 100644
--- a/tools/kallisto-quant.nix
+++ b/tools/kallisto-quant.nix
@@ -1,5 +1,5 @@
-{bionix
-, indexFlags ? {}
+{ bionix
+, indexFlags ? { }
 , bias ? false
 , bootstrapSamples ? 0
 , seed ? 42
@@ -10,7 +10,8 @@
 , rfStranded ? false
 , fragmentLength ? null
 , fragmentSD ? null
-, ref}:
+, ref
+}:
 
 with bionix;
 with lib;
@@ -21,7 +22,7 @@ inputs:
 
 let
   inherit (bionix.types) matchFiletype';
-  isFastQ = matchFiletype' "kallisto-quant" {fq = _: true; gz = isFastQ; };
+  isFastQ = matchFiletype' "kallisto-quant" { fq = _: true; gz = isFastQ; };
 
   empty = ./kallisto-quant-empty.h5;
 
@@ -45,7 +46,7 @@ let
 
 in
 
-assert (all (x: isFastQ (x.filetype)) inputs);
+assert (all (x: isFastQ x.filetype) inputs);
 
 stage {
   name = "kallisto-quant";
diff --git a/tools/kallisto.nix b/tools/kallisto.nix
index 13de61e..e096d11 100644
--- a/tools/kallisto.nix
+++ b/tools/kallisto.nix
@@ -1,4 +1,4 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
@@ -6,7 +6,7 @@ with bionix;
   index = callBionixE ./kallisto-index.nix;
 
   /* Quantify reads against a transcriptome
-  Type: { bias :: bool, bootstrapSamples :: int, seed :: int, plaintext :: bool, fusion :: bool, single :: bool, frStranded :: bool, rfStranded :: bool, fragmentLength :: Int, fragmentSD :: real } -> [fastq] -> kallisto
+    Type: { bias :: bool, bootstrapSamples :: int, seed :: int, plaintext :: bool, fusion :: bool, single :: bool, frStranded :: bool, rfStranded :: bool, fragmentLength :: Int, fragmentSD :: real } -> [fastq] -> kallisto
   */
   quant = callBionixE ./kallisto-quant.nix;
 }
diff --git a/tools/last-align.nix b/tools/last-align.nix
index b2c8460..b326877 100644
--- a/tools/last-align.nix
+++ b/tools/last-align.nix
@@ -1,7 +1,7 @@
 { bionix
 , ref
 , flags ? null
-, indexAttrs ? {}
+, indexAttrs ? { }
 }:
 
 { input1
@@ -16,10 +16,11 @@ let
   fa = f: matchFiletype "last-ref" { fa = _: f; } f;
   fq = f: matchFiletype "last-input" { fq = _: f; } f;
   fqfa = f: matchFiletype "last-input" { fq = _: f; fa = _: f; } f;
-  Q = f: matchFiletype "last-input" { fq = _: 1; fa = _: 0; } f;
-  parallel = f: matchFiletype "last-input" { fq = _: "parallel-fastq"; fa = _: "parallel-fasta"; } f;
+  Q = matchFiletype "last-input" { fq = _: 1; fa = _: 0; };
+  parallel = matchFiletype "last-input" { fq = _: "parallel-fastq"; fa = _: "parallel-fasta"; };
 
-in stage {
+in
+stage {
   name = "last-align";
   buildInputs = with pkgs; [ last ];
   buildCommand = ''
diff --git a/tools/last.nix b/tools/last.nix
index 3755bde..870bfe6 100644
--- a/tools/last.nix
+++ b/tools/last.nix
@@ -4,7 +4,7 @@ with bionix;
 
 rec {
   /* Align reads against a reference genome
-  Type: { ref :: fastq, ... } -> { input1, input2} -> last
+    Type: { ref :: fastq, ... } -> { input1, input2} -> last
   */
   align = callBionixE ./last-align.nix;
   index = callBionixE ./last-index.nix;
diff --git a/tools/lumpy-call.nix b/tools/lumpy-call.nix
index fffc329..56ac650 100644
--- a/tools/lumpy-call.nix
+++ b/tools/lumpy-call.nix
@@ -21,7 +21,8 @@ let
       '';
     };
 
-in assert (length (unique refs) == 1);
+in
+assert (length (unique refs) == 1);
 
 stage {
   name = "lumpy";
@@ -36,5 +37,5 @@ stage {
       ${flags} \
       -o $out
   '';
-  passthru.filetype = filetype.vcf { ref = ref; };
+  passthru.filetype = filetype.vcf { inherit ref; };
 }
diff --git a/tools/lumpy.nix b/tools/lumpy.nix
index f82134e..59c968f 100644
--- a/tools/lumpy.nix
+++ b/tools/lumpy.nix
@@ -4,7 +4,7 @@ with bionix;
 
 {
   /* Call structural variants
-  Type: { ... } -> [bam] -> vcf
+    Type: { ... } -> [bam] -> vcf
   */
   call = callBionixE ./lumpy-call.nix;
 }
diff --git a/tools/manta-call.nix b/tools/manta-call.nix
index 099d5e6..21cbeba 100644
--- a/tools/manta-call.nix
+++ b/tools/manta-call.nix
@@ -1,6 +1,6 @@
-{ bionix, indexAttrs ? {}, faidxAttrs ? {}, flags ? "" }:
+{ bionix, indexAttrs ? { }, faidxAttrs ? { }, flags ? "" }:
 
-{ normals ? [], tumour ? null }:
+{ normals ? [ ], tumour ? null }:
 
 with bionix;
 with lib;
@@ -8,7 +8,7 @@ with types;
 
 let
   getref = matchFiletype "manta-call" { bam = x: x.ref; };
-  refs = map getref normals ++ optionals (tumour != null) [(getref tumour)];
+  refs = map getref normals ++ optionals (tumour != null) [ (getref tumour) ];
   ref = head refs;
 
   renameAndIndex = f: stage {
diff --git a/tools/manta.nix b/tools/manta.nix
index b34753f..dba8669 100644
--- a/tools/manta.nix
+++ b/tools/manta.nix
@@ -4,7 +4,7 @@ with bionix;
 
 {
   /* Call structural variants
-  Type: { ... } -> { normals :: [bam], tumour :: bam } -> manta
+    Type: { ... } -> { normals :: [bam], tumour :: bam } -> manta
   */
   call = callBionixE ./manta-call.nix;
 }
diff --git a/tools/minimap2-align.nix b/tools/minimap2-align.nix
index a6de0b7..18bca35 100644
--- a/tools/minimap2-align.nix
+++ b/tools/minimap2-align.nix
@@ -18,7 +18,8 @@ let
   fa = f: matchFiletype "minimap2-ref" { fa = _: f; } f;
   fq = f: matchFiletype "minimap2-input" { fq = _: f; gz = matchFiletype' "minimap2-input" { fq = _: f; }; } f;
 
-in stage {
+in
+stage {
   name = "minimap2-align";
   buildInputs = with pkgs; [ minimap2 bc ] ++ optional bamOutput samtools;
   buildCommand = ''
@@ -32,6 +33,6 @@ in stage {
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.none {};};
+  passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.none { }; };
   passthru.multicore = true;
 }
diff --git a/tools/minimap2.nix b/tools/minimap2.nix
index e1d6af5..59439ef 100644
--- a/tools/minimap2.nix
+++ b/tools/minimap2.nix
@@ -4,7 +4,7 @@ with bionix;
 
 rec {
   /* Align read against a reference 
-  * Type: align :: {ref :: fasta, bamOutput :: bool, preset :: string, ...} -> {input1, input2} -> bam/sam
+    * Type: align :: {ref :: fasta, bamOutput :: bool, preset :: string, ...} -> {input1, input2} -> bam/sam
   */
   align = callBionixE ./minimap2-align.nix;
 }
diff --git a/tools/mosdepth-depth.nix b/tools/mosdepth-depth.nix
index 2dbfc8d..2a72989 100644
--- a/tools/mosdepth-depth.nix
+++ b/tools/mosdepth-depth.nix
@@ -1,5 +1,5 @@
 { bionix
-, indexAttrs ? {}
+, indexAttrs ? { }
 , flags ? null
 }:
 
diff --git a/tools/mosdepth-plot.nix b/tools/mosdepth-plot.nix
index f98ae23..87eb67f 100644
--- a/tools/mosdepth-plot.nix
+++ b/tools/mosdepth-plot.nix
@@ -7,7 +7,8 @@ with bionix;
 with lib;
 
 { inputs
-, names ? []}:
+, names ? [ ]
+}:
 
 stage {
   name = "mosdepth-plot";
diff --git a/tools/mosdepth.nix b/tools/mosdepth.nix
index cbebdfb..91c30e5 100644
--- a/tools/mosdepth.nix
+++ b/tools/mosdepth.nix
@@ -4,12 +4,12 @@ with bionix;
 
 {
   /* Compute coverage of a reference given an alignemnt
-  Type: { ... } -> bam -> mosdepth
+    Type: { ... } -> bam -> mosdepth
   */
   depth = callBionixE ./mosdepth-depth.nix;
 
   /* Plot sample coverages. Names are optional.
-  Type: { ... } -> { inputs :: [mosdepth], names :: [string] } -> html
+    Type: { ... } -> { inputs :: [mosdepth], names :: [string] } -> html
   */
   plot = callBionixE ./mosdepth-plot.nix;
 }
diff --git a/tools/mutect-app.nix b/tools/mutect-app.nix
index ca78d34..ad1515c 100644
--- a/tools/mutect-app.nix
+++ b/tools/mutect-app.nix
@@ -1,16 +1,19 @@
-{stdenv, fetchurl, makeWrapper, unzip, fetchFromGitHub}:
+{ stdenv, fetchurl, makeWrapper, unzip, fetchFromGitHub }:
 
 let
-  oldnix = import (fetchFromGitHub {
-    owner = "NixOS";
-    repo = "nixpkgs";
-    rev = "83a893c38a83877588e3ca7ccfeabaa973c30acd";
-    sha256 = "0q7214hag7h95irvhkdb648m09b9jspb0raw1qjrx7y4grzb165h";
-  }) {};
+  oldnix = import
+    (fetchFromGitHub {
+      owner = "NixOS";
+      repo = "nixpkgs";
+      rev = "83a893c38a83877588e3ca7ccfeabaa973c30acd";
+      sha256 = "0q7214hag7h95irvhkdb648m09b9jspb0raw1qjrx7y4grzb165h";
+    })
+    { };
 
   jre = oldnix.openjdk7;
 
-in stdenv.mkDerivation rec {
+in
+stdenv.mkDerivation rec {
   name = "mutect-${version}";
   version = "1.1.5";
 
diff --git a/tools/mutect-call.nix b/tools/mutect-call.nix
index e98ba4b..52c1e1d 100644
--- a/tools/mutect-call.nix
+++ b/tools/mutect-call.nix
@@ -1,21 +1,22 @@
-{bionix
+{ bionix
 , cosmic
-, dbsnp}:
+, dbsnp
+}:
 
 with bionix;
 with lib;
 
 let
   inherit (types) matchFiletype;
-  getVCFref = matchFiletype "mutect-call" {vcf = {ref}: ref;};
-  getBAMref = matchFiletype "mutect-call" {bam = {ref, ...}: ref;};
+  getVCFref = matchFiletype "mutect-call" { vcf = { ref }: ref; };
+  getBAMref = matchFiletype "mutect-call" { bam = { ref, ... }: ref; };
   refs = map getVCFref [ cosmic dbsnp ];
   ref = head refs;
 in
 
 assert (length (unique refs) == 1);
 
-{normal, tumour}:
+{ normal, tumour }:
 
 assert (ref == getBAMref normal && ref == getBAMref tumour);
 
diff --git a/tools/mutect.nix b/tools/mutect.nix
index addea77..8f40dee 100644
--- a/tools/mutect.nix
+++ b/tools/mutect.nix
@@ -1,12 +1,12 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
 {
-  app = pkgs.callPackage ./mutect-app.nix {};
+  app = pkgs.callPackage ./mutect-app.nix { };
 
   /* Call somatic variants with mutect
-  Type: { cosmic, dbsnp, ... } -> { normal :: bam, tumour :: bam } -> vcf
+    Type: { cosmic, dbsnp, ... } -> { normal :: bam, tumour :: bam } -> vcf
   */
   call = callBionixE ./mutect-call.nix;
 }
diff --git a/tools/octopus-call.nix b/tools/octopus-call.nix
index 80092e0..81619b6 100644
--- a/tools/octopus-call.nix
+++ b/tools/octopus-call.nix
@@ -18,7 +18,7 @@ with types;
 inputs:
 
 let
-  getref = f: matchFiletype "octopus-call" { bam = { ref, ... }: ref; cram = { ref, ... }: ref; } f;
+  getref = matchFiletype "octopus-call" { bam = { ref, ... }: ref; cram = { ref, ... }: ref; };
   refs = map getref inputs;
   ref = head refs;
 
@@ -63,6 +63,6 @@ stage {
       ${optionalString (targets != null) (handleTarget targets)} \
       ${flags}
   '';
-  passthru.filetype = filetype.vcf { ref = ref; };
+  passthru.filetype = filetype.vcf { inherit ref; };
   passthru.multicore = true;
 }
diff --git a/tools/octopus-callSomatic.nix b/tools/octopus-callSomatic.nix
index 401eeb8..df41550 100644
--- a/tools/octopus-callSomatic.nix
+++ b/tools/octopus-callSomatic.nix
@@ -31,7 +31,7 @@ let
   '';
 
   inputs = [ normal ] ++ tumours;
-  getref = f: matchFiletype "octopus-callSomatic" { bam = { ref, ... }: ref; cram = { ref, ... }: ref; } f;
+  getref = matchFiletype "octopus-callSomatic" { bam = { ref, ... }: ref; cram = { ref, ... }: ref; };
   refs = map getref inputs;
   ref = head refs;
 
@@ -77,6 +77,6 @@ stage {
       -N $normal \
       ${flags}
   '';
-  passthru.filetype = filetype.vcf { ref = ref; };
+  passthru.filetype = filetype.vcf { inherit ref; };
   passthru.multicore = true;
 }
diff --git a/tools/octopus.nix b/tools/octopus.nix
index 858d133..7c21758 100644
--- a/tools/octopus.nix
+++ b/tools/octopus.nix
@@ -4,12 +4,12 @@ with bionix;
 
 {
   /* Call variants for a population
-  Type: { fast :: bool, very-fast :: bool, max-genotypes :: int, targets :: FilePath + [string], ... } -> [bam] -> vcf
+    Type: { fast :: bool, very-fast :: bool, max-genotypes :: int, targets :: FilePath + [string], ... } -> [bam] -> vcf
   */
   call = callBionixE ./octopus-call.nix;
-   
+
   /* Call somatic variants
-  Type: { fast :: bool, very-fast :: bool, max-genotypes :: int, targets :: FilePath + [string], ... } -> { normal :: bam, tumours :: [bam] } -> vcf
+    Type: { fast :: bool, very-fast :: bool, max-genotypes :: int, targets :: FilePath + [string], ... } -> { normal :: bam, tumours :: [bam] } -> vcf
   */
   callSomatic = callBionixE ./octopus-callSomatic.nix;
 }
diff --git a/tools/picard-markDuplicates.nix b/tools/picard-markDuplicates.nix
index 957a05e..e4b6369 100644
--- a/tools/picard-markDuplicates.nix
+++ b/tools/picard-markDuplicates.nix
@@ -1,8 +1,8 @@
 { bionix
 , flags ? null
-} :
+}:
 
-inputBam :
+inputBam:
 
 with bionix;
 with lib;
@@ -10,24 +10,24 @@ with types;
 
 assert (matchFiletype "picard-markDuplicates" { bam = _: true; } inputBam);
 assert (matchFileSorting
-    "picard-markDuplicates"
-    { coord = _: true; name = _: true; }
-    inputBam);
+  "picard-markDuplicates"
+  { coord = _: true; name = _: true; }
+  inputBam);
 
 # Note that picard markDuplicates has different behaviour depending on whether the input
 # is name-sorted or coordinate-sorted.
 
 stage {
-    name = "picard-markDuplicates";
-    buildInputs = with pkgs;
-        [ picard-tools ];
-    outputs = [ "out" "metrics" ];
-    buildCommand = ''
-        picard MarkDuplicates \
-            I=${inputBam} \
-            O=$out \
-            M=$metrics \
-            ${optionalString (flags != null) flags}
-        '';
-    passthru.filetype = inputBam.filetype;
+  name = "picard-markDuplicates";
+  buildInputs = with pkgs;
+    [ picard-tools ];
+  outputs = [ "out" "metrics" ];
+  buildCommand = ''
+    picard MarkDuplicates \
+        I=${inputBam} \
+        O=$out \
+        M=$metrics \
+        ${optionalString (flags != null) flags}
+  '';
+  passthru.filetype = inputBam.filetype;
 }
diff --git a/tools/picard.nix b/tools/picard.nix
index 4246afe..3cb61a1 100644
--- a/tools/picard.nix
+++ b/tools/picard.nix
@@ -3,8 +3,8 @@
 with bionix;
 
 {
-    /* Mark duplicates
+  /* Mark duplicates
     Type: { ... } -> bam -> bam
-    */
-    markDuplicates = callBionixE ./picard-markDuplicates.nix;
-}
\ No newline at end of file
+  */
+  markDuplicates = callBionixE ./picard-markDuplicates.nix;
+}
diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
index bb0faf1..59a224b 100644
--- a/tools/platypus-callVariants.nix
+++ b/tools/platypus-callVariants.nix
@@ -1,6 +1,6 @@
 { bionix
-, indexAttrs ? {}
-, bamIndexAttrs ? {}
+, indexAttrs ? { }
+, bamIndexAttrs ? { }
 , flags ? null
 }:
 
@@ -13,7 +13,7 @@ with types;
 
 let
   filename = path: last (splitString "/" path);
-  getref = f: matchFiletype "platypus-callVariants" { bam = {ref, ...}: ref; } f;
+  getref = matchFiletype "platypus-callVariants" { bam = { ref, ... }: ref; };
   refs = map getref inputs;
   ref = head refs;
 in
@@ -38,6 +38,6 @@ stage {
     # Remove timestamps from output
     sed -i '/^##fileDate/d' $out
   '';
-  passthru.filetype = filetype.vcf {ref = ref;};
+  passthru.filetype = filetype.vcf { inherit ref; };
   passthru.multicore = true;
 }
diff --git a/tools/platypus.nix b/tools/platypus.nix
index c93a2d8..29e7e08 100644
--- a/tools/platypus.nix
+++ b/tools/platypus.nix
@@ -4,7 +4,7 @@ with bionix;
 
 {
   /* Call variants 
-  Type: { ... } -> [bam] -> vcf
+    Type: { ... } -> [bam] -> vcf
   */
   call = callBionixE ./platypus-callVariants.nix;
 }
diff --git a/tools/sambamba.nix b/tools/sambamba.nix
index 3c1d1fd..77289fe 100644
--- a/tools/sambamba.nix
+++ b/tools/sambamba.nix
@@ -5,34 +5,35 @@ with bionix;
 let
   gen = callBionixE ./sambamba-generic.nix;
 
-in {
+in
+{
   /* Sort aligned reads
-  Type: { nameSort :: bool, ... } -> bam -> bam
+    Type: { nameSort :: bool, ... } -> bam -> bam
   */
   sort = callBionixE ./sambamba-sort.nix;
 
   /* Build an index
-  Type: { ... } -> bam -> index
+    Type: { ... } -> bam -> index
   */
-  index = def gen {tool = "index"; };
+  index = def gen { tool = "index"; };
 
   /* Merge bam files
-  Type: { ... } -> [bam] -> bam
+    Type: { ... } -> [bam] -> bam
   */
-  merge = def gen {tool = "merge"; };
+  merge = def gen { tool = "merge"; };
 
   /* Slice a region out of a bam file
-  Type: { region, ... } -> bam -> bam
+    Type: { region, ... } -> bam -> bam
   */
-  slice = def gen {tool = "slice"; };
+  slice = def gen { tool = "slice"; };
 
   /* Compute flag statistics
-  Type: { ... } -> bam -> flagstat
+    Type: { ... } -> bam -> flagstat
   */
-  flagstat = def gen {tool = "flagstat"; };
+  flagstat = def gen { tool = "flagstat"; };
 
   /* Mark duplicates
-  Type: { ... } -> bam -> bam
+    Type: { ... } -> bam -> bam
   */
-  markdup = def gen {tool = "markdup"; };
+  markdup = def gen { tool = "markdup"; };
 }
diff --git a/tools/samtools-merge.nix b/tools/samtools-merge.nix
index 792ee52..ff8ea00 100644
--- a/tools/samtools-merge.nix
+++ b/tools/samtools-merge.nix
@@ -10,8 +10,8 @@ with lib;
 
 let
   inherit (bionix.types) matchFiletype matchSorting;
-  inputIsHomogenous = length (unique (map (matchFiletype "samtools-merge" {bam = x: x // {sorting = matchSorting "samtools-merge" {coord = _: "coord"; name = _: "name"; } x;};}) inputs)) == 1;
-  nameSorted = matchFiletype "samtools-merge" { bam = x: matchSorting "samtools-merge" {coord = _: false; name = _: true;} x;} (lib.head inputs);
+  inputIsHomogenous = length (unique (map (matchFiletype "samtools-merge" { bam = x: x // { sorting = matchSorting "samtools-merge" { coord = _: "coord"; name = _: "name"; } x; }; }) inputs)) == 1;
+  nameSorted = matchFiletype "samtools-merge" { bam = matchSorting "samtools-merge" { coord = _: false; name = _: true; }; } (lib.head inputs);
 in
 
 assert inputIsHomogenous;
diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix
index e3fbff8..30439f1 100644
--- a/tools/samtools-sort.nix
+++ b/tools/samtools-sort.nix
@@ -17,9 +17,10 @@ assert (matchFiletype "samtools-sort" { bam = _: true; sam = _: true; cram = _:
 
 let
   outfmtR = if outfmt != null then outfmt input else input.filetype;
-  outFmtFlags = matchFiletype "samtools-sort-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = ref: "-O CRAM -T ${ref}"; } {filetype = outfmtR;};
-  alreadySorted = matchFileSorting "samtools-sort" { name = _: nameSort; coord = _: !nameSort; none = _: false;} input;
-in stage {
+  outFmtFlags = matchFiletype "samtools-sort-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = ref: "-O CRAM -T ${ref}"; } { filetype = outfmtR; };
+  alreadySorted = matchFileSorting "samtools-sort" { name = _: nameSort; coord = _: !nameSort; none = _: false; } input;
+in
+stage {
   name = "samtools-sort";
   buildInputs = with pkgs; [ samtools ];
   buildCommand =
diff --git a/tools/samtools-view.nix b/tools/samtools-view.nix
index 35a3fcb..4d2bdc7 100644
--- a/tools/samtools-view.nix
+++ b/tools/samtools-view.nix
@@ -15,8 +15,9 @@ assert (matchFiletype "samtools-view" { bam = _: true; sam = _: true; cram = _:
 let
   outfmtR = if outfmt != null then (if builtins.typeOf outfmt == "string" then { "bam" = toBam; "cram" = toCram; "sam" = toSam; }."${outfmt}" else outfmt) input else input.filetype;
   fa = ref: matchFiletype "samtools-view-ref" { fa = _: ref; } ref;
-  outfmtFlags = matchFiletype "samtools-view-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = x: "-O CRAM -T ${fa x.ref}"; } {filetype = outfmtR;};
-in stage {
+  outfmtFlags = matchFiletype "samtools-view-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = x: "-O CRAM -T ${fa x.ref}"; } { filetype = outfmtR; };
+in
+stage {
   name = "samtools-view";
   buildInputs = with pkgs; [ samtools ];
   buildCommand = ''
diff --git a/tools/snap-align.nix b/tools/snap-align.nix
index 279cf20..f0bcb21 100644
--- a/tools/snap-align.nix
+++ b/tools/snap-align.nix
@@ -2,7 +2,7 @@
 , ref
 , bamOutput ? true
 , flags ? null
-, indexAttrs ? {}
+, indexAttrs ? { }
 }:
 
 { input1
@@ -18,7 +18,8 @@ let
   fa = f: matchFiletype "snap-ref" { fa = _: f; } f;
   fq = f: matchFiletype "snap-input" { fq = _: f; gz = matchFiletype' "snap-input" { fq = _: f; }; } f;
 
-in stage {
+in
+stage {
   name = "snap-align";
   buildInputs = with pkgs; [ bionix.snap.app bc ] ++ optional bamOutput samtools;
   buildCommand = ''
@@ -32,6 +33,6 @@ in stage {
       ${optionalString (flags != null) flags} \
       | samtools sort -n > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
 }
diff --git a/tools/snap-app.nix b/tools/snap-app.nix
index c845d1f..0e74a20 100644
--- a/tools/snap-app.nix
+++ b/tools/snap-app.nix
@@ -1,4 +1,4 @@
-{stdenv, fetchFromGitHub, zlib}:
+{ stdenv, fetchFromGitHub, zlib }:
 
 stdenv.mkDerivation rec {
   name = "snap-git";
diff --git a/tools/snap.nix b/tools/snap.nix
index 851c51a..51df5dc 100644
--- a/tools/snap.nix
+++ b/tools/snap.nix
@@ -3,15 +3,15 @@
 with bionix;
 
 rec {
-  app = pkgs.callPackage ./snap-app.nix {};
+  app = pkgs.callPackage ./snap-app.nix { };
 
   /* Align reads against a reference
-  Type: snap :: {ref :: fasta, bamOutput :: bool, ...} -> {input1, input2} -> bam/sam
+    Type: snap :: {ref :: fasta, bamOutput :: bool, ...} -> {input1, input2} -> bam/sam
   */
   align = callBionixE ./snap-align.nix;
 
   /* Creates an reference index for SNAP
-  Type: index :: {...} -> fasta -> SNAP index
+    Type: index :: {...} -> fasta -> SNAP index
   */
   index = callBionixE ./snap-index.nix;
 }
diff --git a/tools/snpeff-annotate.nix b/tools/snpeff-annotate.nix
index 317d303..9324f47 100644
--- a/tools/snpeff-annotate.nix
+++ b/tools/snpeff-annotate.nix
@@ -1,7 +1,8 @@
-{bionix
-,db
-,heapSize ? "31g"
-,flags ? ""}:
+{ bionix
+, db
+, heapSize ? "31g"
+, flags ? ""
+}:
 
 input:
 
diff --git a/tools/snpeff-dbnsfp.nix b/tools/snpeff-dbnsfp.nix
index 518c121..003f7f8 100644
--- a/tools/snpeff-dbnsfp.nix
+++ b/tools/snpeff-dbnsfp.nix
@@ -1,7 +1,8 @@
-{bionix
-,dbnsfp
-,heapSize ? "31g"
-,flags ? ""}:
+{ bionix
+, dbnsfp
+, heapSize ? "31g"
+, flags ? ""
+}:
 
 input:
 
diff --git a/tools/snpeff.nix b/tools/snpeff.nix
index fb3f4a9..45a0edc 100644
--- a/tools/snpeff.nix
+++ b/tools/snpeff.nix
@@ -1,15 +1,15 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
 {
   /* Annotate variants with SNPEff database. Some annotation DBs available in bionix.ref (e.g., bionix.ref.grch38.snpeff.db).
-  Type: { db, ... } -> vcf -> vcf
+    Type: { db, ... } -> vcf -> vcf
   */
   annotate = callBionixE ./snpeff-annotate.nix;
-  
+
   /* Annotate variants with dbNSFP database. Some dbNSFP annotation DBs available in bionix.ref (e.g., bionix.ref.grch38.snpeff.dbNSFP).
-  Type: { dbnsfp, ... } -> vcf -> vcf
+    Type: { dbnsfp, ... } -> vcf -> vcf
   */
   dbnsfp = callBionixE ./snpeff-dbnsfp.nix;
 }
diff --git a/tools/snver-call.nix b/tools/snver-call.nix
index 72562c7..2ad4b72 100644
--- a/tools/snver-call.nix
+++ b/tools/snver-call.nix
@@ -11,7 +11,7 @@ with types;
 
 let
   config = pkgs.writeText "pool.txt" (concatMapStringsSep "\n" (x: "${x}\t${toString ploidy}\t1") (attrValues inputs));
-  getref = f: matchFiletype "SNVer-call" { bam = {ref, ...}: ref; } f;
+  getref = matchFiletype "SNVer-call" { bam = { ref, ... }: ref; };
   refs = mapAttrsToList (_: getref) inputs;
   ref = head refs;
 in
diff --git a/tools/snver.nix b/tools/snver.nix
index 6f95e1b..c5799ec 100644
--- a/tools/snver.nix
+++ b/tools/snver.nix
@@ -4,10 +4,10 @@ with bionix;
 with pkgs;
 
 {
-  app = callPackage ./snver-app.nix {};
+  app = callPackage ./snver-app.nix { };
 
   /* Call variants
-  Type: { ploidy, ... } -> [bam] -> vcf
+    Type: { ploidy, ... } -> [bam] -> vcf
   */
   call = callBionix ./snver-call.nix;
 }
diff --git a/tools/star-align.nix b/tools/star-align.nix
index 44dd7f2..670c6bf 100644
--- a/tools/star-align.nix
+++ b/tools/star-align.nix
@@ -2,7 +2,7 @@
 , ref
 , bamOutput ? true
 , flags ? null
-, indexAttrs ? {}
+, indexAttrs ? { }
 }:
 
 { input1
@@ -18,7 +18,8 @@ let
   fa = f: matchFiletype "star-ref" { fa = _: f; } f;
   fq = f: matchFiletype "star-input" { fq = _: f; gz = matchFiletype' "star-input" { fq = _: "<(gunzip < ${f})"; }; } f;
 
-in stage {
+in
+stage {
   name = "star-align";
   buildInputs = with pkgs; [ star bc samtools ];
   buildCommand = ''
@@ -33,6 +34,6 @@ in stage {
      --readFilesIn ${fq input1} ${optionalString (input2 != null) (fq input2)}
      ${if bamOutput then "samtools view -b Aligned.out.sam > $out" else "cp Aligned.out.sam $out"}
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
 }
diff --git a/tools/star-index.nix b/tools/star-index.nix
index 4bc8399..9b7c819 100644
--- a/tools/star-index.nix
+++ b/tools/star-index.nix
@@ -1,8 +1,8 @@
 { bionix
 , gtf
 , flags ? null
-, extractSpliceSitesAttrs ? {}
-, extractExonsAttrs ? {}
+, extractSpliceSitesAttrs ? { }
+, extractExonsAttrs ? { }
 , overhang ? 100
 }:
 
diff --git a/tools/star.nix b/tools/star.nix
index 744c4e0..1209d4d 100644
--- a/tools/star.nix
+++ b/tools/star.nix
@@ -4,7 +4,7 @@ with bionix;
 
 {
   /* Align RNA against a reference genome
-  Type: { ref, ... } -> { input1, input2 } -> bam
+    Type: { ref, ... } -> { input1, input2 } -> bam
   */
   align = callBionixE ./star-align.nix;
   index = callBionixE ./star-index.nix;
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index 74dfd0b..6a84b24 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -1,6 +1,6 @@
 { bionix
-, indexAttrs ? {}
-, bamIndexAttrs ? {}
+, indexAttrs ? { }
+, bamIndexAttrs ? { }
 , flags ? null
 }:
 
@@ -12,7 +12,7 @@ with types;
 
 let
   filename = path: last (splitString "/" path);
-  getref = f: matchFiletype "strelka-call" { bam = x: x.ref; } f;
+  getref = matchFiletype "strelka-call" { bam = x: x.ref; };
   refs = map getref inputs;
   ref = head refs;
 
@@ -21,38 +21,39 @@ in
 assert (length (unique refs) == 1);
 
 let
-out = stage {
-  name = "strelka-call";
-  buildInputs = with pkgs; [ strelka ];
-  buildCommand = ''
-    ln -s ${ref} ref.fa
-    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 ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
+  out = stage {
+    name = "strelka-call";
+    buildInputs = with pkgs; [ strelka ];
+    buildCommand = ''
+      ln -s ${ref} ref.fa
+      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 ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
 
-    configureStrelkaGermlineWorkflow.py \
-      ${concatMapStringsSep " " (i: "--bam ${filename i}.bam") inputs} \
-      --ref ref.fa \
-      --runDir $TMPDIR
+      configureStrelkaGermlineWorkflow.py \
+        ${concatMapStringsSep " " (i: "--bam ${filename i}.bam") inputs} \
+        --ref ref.fa \
+        --runDir $TMPDIR
 
-    ./runWorkflow.py \
-      -m local \
-      -j $NIX_BUILD_CORES 2>&1
+      ./runWorkflow.py \
+        -m local \
+        -j $NIX_BUILD_CORES 2>&1
 
-    # Strelka writes runtime stats and timestamps;
-    # both have to be stripped to provide determinism
-    cd results/variants
-    rm *.tbi genome.vcf.gz
-    for f in *.vcf.gz; do
-      gunzip $f
-      g=$(basename $f .gz)
-      sed -i '/^##fileDate/d' $g
-      sed -i '/^##startTime/d' $g
-      sed -i '/^##cmd/d' $g
-    done
-    mv variants.vcf $out
-  '';
-  passthru.multicore = true;
-  passthru.filetype = types.filetype.vcf {ref = ref;};
-};
-in out
+      # Strelka writes runtime stats and timestamps;
+      # both have to be stripped to provide determinism
+      cd results/variants
+      rm *.tbi genome.vcf.gz
+      for f in *.vcf.gz; do
+        gunzip $f
+        g=$(basename $f .gz)
+        sed -i '/^##fileDate/d' $g
+        sed -i '/^##startTime/d' $g
+        sed -i '/^##cmd/d' $g
+      done
+      mv variants.vcf $out
+    '';
+    passthru.multicore = true;
+    passthru.filetype = types.filetype.vcf { inherit ref; };
+  };
+in
+out
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix
index b409344..6a8f252 100644
--- a/tools/strelka-callSomatic.nix
+++ b/tools/strelka-callSomatic.nix
@@ -1,10 +1,10 @@
 { bionix
-, indexAttrs ? {}
-, bamIndexAttrs ? {}
+, indexAttrs ? { }
+, bamIndexAttrs ? { }
 , flags ? null
 }:
 
-{normal, tumour}:
+{ normal, tumour }:
 
 with bionix;
 with lib;
@@ -12,7 +12,7 @@ with types;
 
 let
   filename = path: last (splitString "/" path);
-  getref = f: matchFiletype "strelka-callSomatic" { bam = x: x.ref; } f;
+  getref = matchFiletype "strelka-callSomatic" { bam = x: x.ref; };
   inputs = [ normal tumour ];
   refs = map getref inputs;
   ref = head refs;
@@ -23,44 +23,45 @@ assert (length (unique refs) == 1);
 
 let
 
-out = stage {
-  name = "strelka-callSomatic";
-  buildInputs = with pkgs; [ strelka ];
-  outputs = [ "out" "indels" "snvs" ];
-  buildCommand = ''
-    ln -s ${ref} ref.fa
-    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 ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
+  out = stage {
+    name = "strelka-callSomatic";
+    buildInputs = with pkgs; [ strelka ];
+    outputs = [ "out" "indels" "snvs" ];
+    buildCommand = ''
+      ln -s ${ref} ref.fa
+      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 ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
 
-    configureStrelkaSomaticWorkflow.py \
-      --normalBam ${filename normal}.bam \
-      --tumourBam ${filename tumour}.bam \
-      --ref ref.fa \
-      --runDir $TMPDIR
+      configureStrelkaSomaticWorkflow.py \
+        --normalBam ${filename normal}.bam \
+        --tumourBam ${filename tumour}.bam \
+        --ref ref.fa \
+        --runDir $TMPDIR
 
-    ./runWorkflow.py \
-      -m local \
-      -j $NIX_BUILD_CORES
+      ./runWorkflow.py \
+        -m local \
+        -j $NIX_BUILD_CORES
 
-    # Strelka writes runtime stats and timestamps;
-    # both have to be stripped to provide determinism
-    cd results/variants
-    rm *.tbi
-    for f in *.vcf.gz; do
-      gunzip $f
-      g=$(basename $f .gz)
-      sed -i '/^##fileDate/d' $g
-      sed -i '/^##startTime/d' $g
-      sed -i '/^##cmd/d' $g
-    done
-    mv somatic.indels.vcf $indels
-    mv somatic.snvs.vcf $snvs
+      # Strelka writes runtime stats and timestamps;
+      # both have to be stripped to provide determinism
+      cd results/variants
+      rm *.tbi
+      for f in *.vcf.gz; do
+        gunzip $f
+        g=$(basename $f .gz)
+        sed -i '/^##fileDate/d' $g
+        sed -i '/^##startTime/d' $g
+        sed -i '/^##cmd/d' $g
+      done
+      mv somatic.indels.vcf $indels
+      mv somatic.snvs.vcf $snvs
 
-    ln -s $snvs $out
-  '';
-  passthru.multicore = true;
-  passthru.filetype = types.filetype.vcf {ref = ref;};
-};
+      ln -s $snvs $out
+    '';
+    passthru.multicore = true;
+    passthru.filetype = types.filetype.vcf { inherit ref; };
+  };
 
-in out
+in
+out
diff --git a/tools/strelka.nix b/tools/strelka.nix
index 16f4a2b..c71f07b 100644
--- a/tools/strelka.nix
+++ b/tools/strelka.nix
@@ -5,11 +5,11 @@ with types;
 
 {
   /* Calls somatic variants
-  Type: callSomatic :: {...} -> {tumour, normal} -> somatic results
+    Type: callSomatic :: {...} -> {tumour, normal} -> somatic results
   */
   callSomatic = callBionixE ./strelka-callSomatic.nix;
   /* Calls variants
-  Type: call :: {...} -> [input] -> results
+    Type: call :: {...} -> [input] -> results
   */
   call = callBionixE ./strelka-call.nix;
 }
diff --git a/tools/whisper-align.nix b/tools/whisper-align.nix
index 1731bfe..19eef0d 100644
--- a/tools/whisper-align.nix
+++ b/tools/whisper-align.nix
@@ -2,7 +2,7 @@
 , ref
 , bamOutput ? true
 , flags ? null
-, indexAttrs ? {}
+, indexAttrs ? { }
 }:
 
 { input1
@@ -18,7 +18,8 @@ let
   fa = f: matchFiletype "whisper-ref" { fa = _: f; } f;
   fq = f: matchFiletype "whisper-input" { fq = _: f; gz = matchFiletype' "whisper-input" { fq = _: f; }; } f;
 
-in stage {
+in
+stage {
   name = "whisper-mem";
   buildInputs = with pkgs; [ whisper ];
   buildCommand = ''
@@ -34,6 +35,6 @@ in stage {
       ${optionalString (input2 != null) (fq input2)} \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
 }
diff --git a/tools/whisper.nix b/tools/whisper.nix
index ff56f8a..8b89cb2 100644
--- a/tools/whisper.nix
+++ b/tools/whisper.nix
@@ -6,7 +6,7 @@ rec {
   index = callBionixE ./whisper-index.nix;
 
   /* Align reads against a reference
-  Type: { ref, ... } -> { input1, input2 } -> bam
+    Type: { ref, ... } -> { input1, input2 } -> bam
   */
   align = callBionixE ./whisper-align.nix;
 }
diff --git a/tools/xenomapper-allocate.nix b/tools/xenomapper-allocate.nix
index 3c0fc08..adac472 100644
--- a/tools/xenomapper-allocate.nix
+++ b/tools/xenomapper-allocate.nix
@@ -2,7 +2,7 @@
 , flags ? null
 }:
 
-{primary, secondary}:
+{ primary, secondary }:
 
 with bionix;
 with lib;
@@ -10,8 +10,8 @@ with types;
 
 let
 
-  isSortedBam = matchFiletype "xenomapper-allocate" {bam = matchSorting "xenomapper-allocate" { coord = _: false; name = _: true; none = _: false; }; };
-  outs = [ "primary_specific" "primary_multi" "secondary_specific" "secondary_multi" "unassigned" "unresolved"];
+  isSortedBam = matchFiletype "xenomapper-allocate" { bam = matchSorting "xenomapper-allocate" { coord = _: false; name = _: true; none = _: false; }; };
+  outs = [ "primary_specific" "primary_multi" "secondary_specific" "secondary_multi" "unassigned" "unresolved" ];
 
 in
 
diff --git a/tools/xenomapper.nix b/tools/xenomapper.nix
index d22f84b..5ac903e 100644
--- a/tools/xenomapper.nix
+++ b/tools/xenomapper.nix
@@ -1,10 +1,10 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
 {
   /* Split aligned reads based on primary and secondary alignments
-  Type: { ... } -> { primary :: bam, secondary :: bam } -> { primary_specific :: bam, primary_multi :: bam, secondary_specific :: bam, secondary_multi :: bam, unassigned :: bam, unresolved :: bam }
+    Type: { ... } -> { primary :: bam, secondary :: bam } -> { primary_specific :: bam, primary_multi :: bam, secondary_specific :: bam, secondary_multi :: bam, unassigned :: bam, unresolved :: bam }
   */
   allocate = callBionixE ./xenomapper-allocate.nix;
-}
\ No newline at end of file
+}