treewide reformatting and simplification

- simplify with statix
- reformat with nixpkgs-fmt

104 files changed, 933 insertions, 799 deletions

diff --git a/default.nix b/default.nix
index 1944de0..59357b2 100644
--- a/default.nix
+++ b/default.nix
@@ -5,10 +5,11 @@ let
 
   bionix = nixpkgs.lib.makeExtensible (self:
     let callBionix = file: attrs: import file ({ bionix = self; } // attrs);
-    in with self; {
-      callBionix = callBionix;
+    in
+    with self; {
+      inherit callBionix;
       id = x: x;
-      exec = f: x: y: f x y;
+      exec = id;
       exec' = f: exec (_: f) { };
       exec'' = f: exec' (_: f) { };
       callBionixE = p: exec (callBionix p);
@@ -52,15 +53,17 @@ let
 
       slurm-run = callPackage ./lib/slurm.nix { };
       slurm-exec = f: x: y:
-        slurm-run x (f (builtins.removeAttrs x [
-          "ppn"
-          "mem"
-          "walltime"
-          "partition"
-          "slurmFlags"
-          "salloc"
-          "srun"
-        ]) y);
+        slurm-run x (f
+          (builtins.removeAttrs x [
+            "ppn"
+            "mem"
+            "walltime"
+            "partition"
+            "slurmFlags"
+            "salloc"
+            "srun"
+          ])
+          y);
       slurm = bionix.extend (self: super: { exec = super.slurm-run; });
       qsub = attrs:
         bionix.extend (self: super:
@@ -78,7 +81,8 @@ let
             qsub = attrs: (callPackage ./lib/qsub.nix { }) (qsubDefs // attrs);
             exec = f: x: y:
               qsub (builtins.intersectAttrs qsubDefs x) (super.exec f
-                (builtins.removeAttrs x (builtins.attrNames qsubDefs)) y);
+                (builtins.removeAttrs x (builtins.attrNames qsubDefs))
+                y);
           });
       def = f: defs: attrs: f (defs // attrs);
 
@@ -88,22 +92,24 @@ let
           name = "link-outputs";
           outputs = [ "out" ] ++ attrNames x;
           nativeBuildInputs = [ pkgs.perl ];
-          buildCommand = let
-            recurse = x:
-              if x ? type && x.type == "derivation" then
-                x
-              else if builtins.typeOf x == "set" then
-                linkOutputs x
-              else
-                abort "linkOutputs: unsupported type";
-            link = dst: src: ''
-              ln -s ${recurse src} $(perl -e 'print $ENV{"${dst}"}') ; ln -s ${
-                recurse src
-              } $out/${dst}
-            '';
-          in ''
-            mkdir $out 
-          '' + (concatStringsSep "\n" (mapAttrsToList link x));
+          buildCommand =
+            let
+              recurse = x:
+                if x ? type && x.type == "derivation" then
+                  x
+                else if builtins.typeOf x == "set" then
+                  linkOutputs x
+                else
+                  abort "linkOutputs: unsupported type";
+              link = dst: src: ''
+                ln -s ${recurse src} $(perl -e 'print $ENV{"${dst}"}') ; ln -s ${
+                  recurse src
+                } $out/${dst}
+              '';
+            in
+            ''
+              mkdir $out 
+            '' + (concatStringsSep "\n" (mapAttrsToList link x));
           passthru.linkInputs = x;
         };
 
@@ -127,15 +133,15 @@ let
       # Export nixpkgs and standard library lib
       pkgs = nixpkgs;
       lib = nixpkgs.lib // {
-        types = types;
+        inherit types;
         shard = callBionix ./lib/shard.nix { };
       };
       stage = x@{ name, stripStorePaths ? true, multicore ? false, ... }:
         (if stripStorePaths then strip else x: x)
-        (nixpkgs.stdenvNoCC.mkDerivation (x // {
-          name = "bionix-" + name;
-          inherit multicore;
-        }));
+          (nixpkgs.stdenvNoCC.mkDerivation (x // {
+            name = "bionix-" + name;
+            inherit multicore;
+          }));
       strip = drv:
         let
           stripCommand = ''
@@ -156,7 +162,8 @@ let
               rewriteOutput $o
             done
           '';
-        in drv.overrideAttrs (attrs:
+        in
+        drv.overrideAttrs (attrs:
           if attrs ? buildCommand then {
             buildCommand = attrs.buildCommand + stripCommand;
           } else {
@@ -186,13 +193,15 @@ let
   overlayByType = {
     lambda = bionix: overlay:
       bionix.extend
-      (self: super: nixpkgs.lib.recursiveUpdate super (overlay self super));
+        (self: super: nixpkgs.lib.recursiveUpdate super (overlay self super));
     path = bionix: path: overlay bionix (import path);
   };
   overlay = bionix: overlay:
     let overlayType = builtins.typeOf overlay;
-    in if overlayByType ? ${overlayType} then
-      overlayByType.${overlayType} bionix overlay
+    in
+    if overlayByType ? "${overlayType}" then
+      overlayByType."${overlayType}" bionix overlay
     else
       builtins.throw ("cannot overlay type " + overlayType);
-in with nixpkgs.lib; foldl overlay bionix overlays
+in
+with nixpkgs.lib; foldl overlay bionix overlays
diff --git a/doc/default.nix b/doc/default.nix
index d68a6b1..ac8bfeb 100644
--- a/doc/default.nix
+++ b/doc/default.nix
@@ -1,4 +1,4 @@
-{ bionix ? import ./.. {} }:
+{ bionix ? import ./.. { } }:
 
 with bionix;
 
diff --git a/examples/call.nix b/examples/call.nix
index 8a38fdb..81a112e 100644
--- a/examples/call.nix
+++ b/examples/call.nix
@@ -2,9 +2,10 @@
 # with the Platypus variant caller. Each input is preprocessed by aligning
 # against a reference genome (defaults to GRCH38), fixing mate information, and
 # marking duplicates. Finally platypus is called over all samples.
-{bionix ? import <bionix> {}
-,inputs
-,ref ? bionix.ref.grch38.seq }:
+{ bionix ? import <bionix> { }
+, inputs
+, ref ? bionix.ref.grch38.seq
+}:
 
 with bionix;
 with lib;
@@ -13,9 +14,10 @@ let
   preprocess = flip pipe [
     (bwa.align { inherit ref; })
     (samtools.sort { nameSort = true; })
-    (samtools.fixmate {})
-    (samtools.sort {})
-    (samtools.markdup {})
+    (samtools.fixmate { })
+    (samtools.sort { })
+    (samtools.markdup { })
   ];
 
-in platypus.call {} (map preprocess inputs)
+in
+platypus.call { } (map preprocess inputs)
diff --git a/examples/default.nix b/examples/default.nix
index 9aace38..ef57341 100644
--- a/examples/default.nix
+++ b/examples/default.nix
@@ -1,6 +1,6 @@
 # This example uses the pipelines specified in the call.nix file on the
 # synthetic data in this directory.
-{bionix ? import <bionix> {}}:
+{ bionix ? import <bionix> { } }:
 
 with bionix;
 
@@ -15,7 +15,7 @@ let
         sha256 = "0kh29i6fg14dn0fb1xj6pkpk6d83y7zg7aphkbvjrhm82braqkm8";
       };
 
-      input2 =  fetchFastQ {
+      input2 = fetchFastQ {
         url = "https://github.com/PapenfussLab/bionix/raw/master/examples/sample1-2.fq";
         sha256 = "0czk85km6a91y0fn4b7f9q7ps19b5jf7jzwbly4sgznps7ir2kdk";
       };
@@ -28,7 +28,7 @@ let
         sha256 = "08gixavfklqvk1m2ic6v56z82vl00qnpsd9xb64z6zl03nz98mcy";
       };
 
-      input2 =  fetchFastQ {
+      input2 = fetchFastQ {
         url = "https://github.com/PapenfussLab/bionix/raw/master/examples/sample2-2.fq";
         sha256 = "1xxwm2vq52axpdhm14rh5mg5nzzpxaqnvhzrqhajm27fqksgzjjw";
       };
@@ -41,4 +41,5 @@ let
     sha256 = "0sy9hq8n55knfkiblam50dzaiwhrx6pv8b8l1njdn6kfj4wflz2p";
   };
 
-in import ./call.nix {inherit inputs ref bionix;}
+in
+import ./call.nix { inherit inputs ref bionix; }
diff --git a/examples/ex-nextflow/nextflow-example1.nix b/examples/ex-nextflow/nextflow-example1.nix
index 4f00431..687505c 100644
--- a/examples/ex-nextflow/nextflow-example1.nix
+++ b/examples/ex-nextflow/nextflow-example1.nix
@@ -1,7 +1,8 @@
 # This is a translation of the Nextflow example found at
 # https://www.nextflow.io/example1.html
-{ bionix ? import ./../.. {}
-, input ? ./sample.fa}:
+{ bionix ? import ./../.. { }
+, input ? ./sample.fa
+}:
 
 with bionix;
 with lib;
@@ -24,7 +25,8 @@ let
     '';
   };
 
-in pipe input [
+in
+pipe input [
   splitSequences
   (each reverse)
 ]
diff --git a/examples/ex-tnpair/cluster.nix b/examples/ex-tnpair/cluster.nix
index 8d54995..5d4e1de 100644
--- a/examples/ex-tnpair/cluster.nix
+++ b/examples/ex-tnpair/cluster.nix
@@ -4,11 +4,12 @@ let
   bionix = import <bionix> {
     overlays = [
       (_: super:
-        super."${if tmpDir == null then "slurm" else "qsub"}" {
-          ppn = 24;
-          mem = 7;
-          walltime = "3:00:00";
-        } // super.lib.optionalAttrs (tmpDir != null) { inherit tmpDir; })
+        super."${if tmpDir == null then "slurm" else "qsub"}"
+          {
+            ppn = 24;
+            mem = 7;
+            walltime = "3:00:00";
+          } // super.lib.optionalAttrs (tmpDir != null) { inherit tmpDir; })
 
       (self: super:
         with super; {
@@ -27,4 +28,5 @@ let
         })
     ];
   };
-in import ./. { inherit bionix; }
+in
+import ./. { inherit bionix; }
diff --git a/examples/ex-tnpair/default.nix b/examples/ex-tnpair/default.nix
index f9581f8..65a2265 100644
--- a/examples/ex-tnpair/default.nix
+++ b/examples/ex-tnpair/default.nix
@@ -45,6 +45,7 @@ let
 
   fetch = s: mapAttrs (_: fetchFastQGZ) s.inputs;
 
-in import ./tnpair.nix {
+in
+import ./tnpair.nix {
   inherit pair fetch bionix;
 }
diff --git a/examples/ex-tnpair/tnpair.nix b/examples/ex-tnpair/tnpair.nix
index 9e6befe..414a391 100644
--- a/examples/ex-tnpair/tnpair.nix
+++ b/examples/ex-tnpair/tnpair.nix
@@ -1,4 +1,4 @@
-{bionix ? import <bionix> {}, pair, fetch}:
+{ bionix ? import <bionix> { }, pair, fetch }:
 
 with bionix;
 with lib;
@@ -13,7 +13,7 @@ let
     fetch
     (align { preset = "sr"; ref = ref.grch38.seq; flags = "-R'@RG\\tID:${s.type}\\tSM:${s.type}'"; })
     (sort { nameSort = true; })
-    (fixmate {})
+    (fixmate { })
     (sort { })
     (markdup { })
   ];
@@ -28,21 +28,26 @@ let
 
   bams = mapAttrs (_: preprocess) pair;
 
-  variants = let
-    somatic = strelka.callSomatic { } bams; in mapAttrs (_: flip pipe [
-      (compression.uncompress { })
-      (snpeff.annotate { db = ref.grch38.snpeff.db; })
-      dropErrors
-      (snpeff.dbnsfp { dbnsfp = ref.grch38.snpeff.dbnsfp; })
-    ]) {
-      "snvs.vcf" = somatic.snvs;
-      "indels.vcf" = somatic.snvs;
-      "germline.vcf" = strelka.call { } [bams.normal];
-    };
+  variants =
+    let
+      somatic = strelka.callSomatic { } bams; in
+    mapAttrs
+      (_: flip pipe [
+        (compression.uncompress { })
+        (snpeff.annotate { inherit (ref.grch38.snpeff) db; })
+        dropErrors
+        (snpeff.dbnsfp { inherit (ref.grch38.snpeff) dbnsfp; })
+      ])
+      {
+        "snvs.vcf" = somatic.snvs;
+        "indels.vcf" = somatic.snvs;
+        "germline.vcf" = strelka.call { } [ bams.normal ];
+      };
 
   cnvs = cnvkit.callCNV { } { normals = [ bams.normal ]; tumours = [ bams.tumour ]; };
 
-in linkOutputs {
+in
+linkOutputs {
   inherit variants;
   alignments = linkOutputs (mapAttrs' (n: nameValuePair (n + ".bam")) bams);
   cnvkit = cnvs;
diff --git a/examples/ex-wdl/wdl-scatter-gather.nix b/examples/ex-wdl/wdl-scatter-gather.nix
index 61dc441..5245662 100644
--- a/examples/ex-wdl/wdl-scatter-gather.nix
+++ b/examples/ex-wdl/wdl-scatter-gather.nix
@@ -1,6 +1,6 @@
 # The scatter-gather example from https://github.com/openwdl/wdl
 # translated to bionix
-{ bionix ? import ./../.. {} }:
+{ bionix ? import ./../.. { } }:
 
 with bionix;
 with lib;
@@ -30,4 +30,5 @@ let
     '';
   };
 
-in gather (map analysis prepare)
+in
+gather (map analysis prepare)
diff --git a/lib/google.nix b/lib/google.nix
index 354b5c5..06b80b3 100644
--- a/lib/google.nix
+++ b/lib/google.nix
@@ -10,7 +10,9 @@ let
       "https://raw.githubusercontent.com/circulosmeos/gdown.pl/master/gdown.pl";
     sha256 = "1pw3vg70bgf33akbbphpr6zn3jndv0khmsa3k0m877hgzg1v52qv";
   };
-in runCommand "gdown" {
+in
+runCommand "gdown"
+{
   nativeBuildInputs = [ perl wget ];
   outputHashAlgo = "sha256";
   outputHash = sha256;
diff --git a/lib/qsub.nix b/lib/qsub.nix
index a8827a8..2528162 100644
--- a/lib/qsub.nix
+++ b/lib/qsub.nix
@@ -4,76 +4,87 @@ with lib;
 
 let escape = x: if builtins.typeOf x == "string" then escapeShellArg x else x;
 
-in { ppn, mem, walltime, queue ? null, qsubFlags ? null, tmpDir, sleepTime
-, qsubPath ? "/usr/bin" }:
+in
+{ ppn
+, mem
+, walltime
+, queue ? null
+, qsubFlags ? null
+, tmpDir
+, sleepTime
+, qsubPath ? "/usr/bin"
+}:
 drv:
 let ppnReified = if drv.multicore then ppn else 1;
-in overrideDerivation drv ({ args, builder, name, ... }: {
+in
+overrideDerivation drv ({ args, builder, name, ... }: {
   builder = "/bin/bash";
-  args = let
-    script = writeScript "qsub-script" ''
-      #!${stdenv.shell}
-      while [ ! -e ${tmpDir}/qsub-$PBS_JOBID ] ; do
-        sleep ${toString sleepTime}
-      done
-      set -a
-      . ${tmpDir}/qsub-$PBS_JOBID/nix-set
-      set +a
-      TMPDIR=${tmpDir}/qsub-$PBS_JOBID
-      TEMP=$TMPDIR
-      TMP=$TMPDIR
-      NIX_BUILD_TOP=$TMPDIR
-      cd $TMPDIR
-      ${builder} ${concatMapStringsSep " " escape args} &> qsub-log
-      echo $? > qsub-exit
-    '';
+  args =
+    let
+      script = writeScript "qsub-script" ''
+        #!${stdenv.shell}
+        while [ ! -e ${tmpDir}/qsub-$PBS_JOBID ] ; do
+          sleep ${toString sleepTime}
+        done
+        set -a
+        . ${tmpDir}/qsub-$PBS_JOBID/nix-set
+        set +a
+        TMPDIR=${tmpDir}/qsub-$PBS_JOBID
+        TEMP=$TMPDIR
+        TMP=$TMPDIR
+        NIX_BUILD_TOP=$TMPDIR
+        cd $TMPDIR
+        ${builder} ${concatMapStringsSep " " escape args} &> qsub-log
+        echo $? > qsub-exit
+      '';
 
-    qsub = writeScript "qsub" ''
-      #!${stdenv.shell}
-      PATH=${qsubPath}
-      SHELL=/bin/sh
-      NIX_BUILD_CORES=${toString ppnReified}
+      qsub = writeScript "qsub" ''
+        #!${stdenv.shell}
+        PATH=${qsubPath}
+        SHELL=/bin/sh
+        NIX_BUILD_CORES=${toString ppnReified}
 
-      while : ; do
-        qsub -l nodes=1:ppn=${toString ppnReified},mem=${
-          toString mem
-        }gb,walltime=${walltime} \
-          -N "${name}" \
-          ${optionalString (queue != null) "-q ${queue}"} \
-          ${optionalString (qsubFlags != null) qsubFlags} \
-          ${script} 2>&1 > id
-        if [ $? -eq 0 ] ; then
-          break
-        fi
-        if ! grep "Please retry" id > /dev/null ; then
-          cat id >&2
-          exit 1
-        fi
-        sleep ${toString sleepTime}
-      done
-      id=$(cat id)
-      echo $id
+        while : ; do
+          qsub -l nodes=1:ppn=${toString ppnReified},mem=${
+            toString mem
+          }gb,walltime=${walltime} \
+            -N "${name}" \
+            ${optionalString (queue != null) "-q ${queue}"} \
+            ${optionalString (qsubFlags != null) qsubFlags} \
+            ${script} 2>&1 > id
+          if [ $? -eq 0 ] ; then
+            break
+          fi
+          if ! grep "Please retry" id > /dev/null ; then
+            cat id >&2
+            exit 1
+          fi
+          sleep ${toString sleepTime}
+        done
+        id=$(cat id)
+        echo $id
 
-      function cleanup {
-        qdel $id 2>/dev/null || true
-        sleep ${toString sleepTime}
-        rm -rf ${tmpDir}/qsub-$id
-      }
-      trap cleanup INT TERM EXIT
+        function cleanup {
+          qdel $id 2>/dev/null || true
+          sleep ${toString sleepTime}
+          rm -rf ${tmpDir}/qsub-$id
+        }
+        trap cleanup INT TERM EXIT
 
-      cp -r $TMPDIR ${tmpDir}/qsub-$id
-      set > ${tmpDir}/qsub-$id/nix-set
-      until qstat -f ''${id%%.} 2>&1 | grep "\(Unknown Job\|job_state = C\)" > /dev/null ; do
-        sleep ${toString sleepTime}
-      done
-      cat ${tmpDir}/qsub-$id/qsub-log
-      if [ -e ${tmpDir}/qsub-$id/qsub-exit ]; then
-        exitCode=$(cat ${tmpDir}/qsub-$id/qsub-exit)
-      else
-        exitCode=1
-      fi
-      exit $exitCode
-    '';
+        cp -r $TMPDIR ${tmpDir}/qsub-$id
+        set > ${tmpDir}/qsub-$id/nix-set
+        until qstat -f ''${id%%.} 2>&1 | grep "\(Unknown Job\|job_state = C\)" > /dev/null ; do
+          sleep ${toString sleepTime}
+        done
+        cat ${tmpDir}/qsub-$id/qsub-log
+        if [ -e ${tmpDir}/qsub-$id/qsub-exit ]; then
+          exitCode=$(cat ${tmpDir}/qsub-$id/qsub-exit)
+        else
+          exitCode=1
+        fi
+        exit $exitCode
+      '';
 
-  in [ "-c" qsub ];
+    in
+    [ "-c" qsub ];
 })
diff --git a/lib/references.nix b/lib/references.nix
index 23ccde3..fd8c3cc 100644
--- a/lib/references.nix
+++ b/lib/references.nix
@@ -26,7 +26,7 @@ rec {
       buildInputs = with pkgs; [ gawk ];
       buildCommand = ''
         gunzip < $src | awk '/^[^#]/{print "chr" $0;next}{print}' > $out
-          '';
+      '';
       passthru.filetype = filetype.vcf { ref = seq; };
     };
     encode.blacklist = stage {
@@ -42,28 +42,30 @@ rec {
       '';
     };
 
-    ensembl = let version = "74";
-    in {
-      cdna = stage {
-        name = "ensembl-grch37-cdna-${version}";
-        src = pkgs.fetchurl {
-          url =
-            "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.${version}.cdna.all.fa.gz";
-          sha256 = "1m62hiw17zcxg3sza0aq53885wb8g202j8lc1ilhmkg2izzbyihj";
+    ensembl =
+      let version = "74";
+      in
+      {
+        cdna = stage {
+          name = "ensembl-grch37-cdna-${version}";
+          src = pkgs.fetchurl {
+            url =
+              "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.${version}.cdna.all.fa.gz";
+            sha256 = "1m62hiw17zcxg3sza0aq53885wb8g202j8lc1ilhmkg2izzbyihj";
+          };
+          buildCommand = "gunzip < $src > $out";
+          passthru.filetype = filetype.fa { };
         };
-        buildCommand = "gunzip < $src > $out";
-        passthru.filetype = filetype.fa { };
-      };
-      gtf = stage {
-        name = "ensembl-grch37-gtf-${version}";
-        src = pkgs.fetchurl {
-          url =
-            "ftp://ftp.ensembl.org/pub/release-${version}/gtf/homo_sapiens/Homo_sapiens.GRCh37.${version}.gtf.gz";
-          sha256 = "1m62hiw17zcxg3sza0aq53885wb8g202j8lc1ilhmkg2izzbyihj";
+        gtf = stage {
+          name = "ensembl-grch37-gtf-${version}";
+          src = pkgs.fetchurl {
+            url =
+              "ftp://ftp.ensembl.org/pub/release-${version}/gtf/homo_sapiens/Homo_sapiens.GRCh37.${version}.gtf.gz";
+            sha256 = "1m62hiw17zcxg3sza0aq53885wb8g202j8lc1ilhmkg2izzbyihj";
+          };
+          buildCommand = "gunzip < $src > $out";
         };
-        buildCommand = "gunzip < $src > $out";
       };
-    };
     snpeff = {
       db = pkgs.stdenv.mkDerivation rec {
         name = "GRCh37.75";
@@ -114,7 +116,7 @@ rec {
       buildInputs = with pkgs; [ gawk ];
       buildCommand = ''
         gunzip < $src | awk '/^[^#]/{print "chr" $0;next}{print}' > $out
-          '';
+      '';
       passthru.filetype = filetype.vcf { ref = seq; };
     };
     encode.blacklist = stage {
@@ -129,47 +131,49 @@ rec {
         gunzip < $bed | awk '{print $1 ":" $2 "-" $3}' > $out
       '';
     };
-    ensembl = let version = "97";
-    in {
-      cdna = stage {
-        name = "ensembl-grch38-cdna-${version}";
-        src = pkgs.fetchurl {
-          url =
-            "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz";
-          sha256 = "1m6hvnvlrsi6bzcmq0lnv0igy3in1a7jp723yc74g4g6zjp3cy8c";
+    ensembl =
+      let version = "97";
+      in
+      {
+        cdna = stage {
+          name = "ensembl-grch38-cdna-${version}";
+          src = pkgs.fetchurl {
+            url =
+              "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz";
+            sha256 = "1m6hvnvlrsi6bzcmq0lnv0igy3in1a7jp723yc74g4g6zjp3cy8c";
+          };
+          buildCommand = "gunzip < $src > $out";
+          passthru.filetype = filetype.fa { };
         };
-        buildCommand = "gunzip < $src > $out";
-        passthru.filetype = filetype.fa { };
-      };
-      ncrna = stage {
-        name = "ensembl-grch38-ncrna-${version}";
-        src = pkgs.fetchurl {
-          url =
-            "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz";
-          sha256 = "1r0dmybn31wf6xc90z2c08ngivkv39hqa8wqg3vik6s4spwpdhj0";
+        ncrna = stage {
+          name = "ensembl-grch38-ncrna-${version}";
+          src = pkgs.fetchurl {
+            url =
+              "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz";
+            sha256 = "1r0dmybn31wf6xc90z2c08ngivkv39hqa8wqg3vik6s4spwpdhj0";
+          };
+          buildCommand = "gunzip < $src > $out";
+          passthru.filetype = filetype.fa { };
         };
-        buildCommand = "gunzip < $src > $out";
-        passthru.filetype = filetype.fa { };
-      };
-      gtf = stage {
-        name = "ensembl-grch38-gtf-${version}";
-        src = pkgs.fetchurl {
-          url =
-            "ftp://ftp.ensembl.org/pub/release-${version}/gtf/homo_sapiens/Homo_sapiens.GRCh38.${version}.gtf.gz";
-          sha256 = "068ab5jf87il301jcr0576c4q0smv6kxpv94gnrm3qzl6kvmaawd";
+        gtf = stage {
+          name = "ensembl-grch38-gtf-${version}";
+          src = pkgs.fetchurl {
+            url =
+              "ftp://ftp.ensembl.org/pub/release-${version}/gtf/homo_sapiens/Homo_sapiens.GRCh38.${version}.gtf.gz";
+            sha256 = "068ab5jf87il301jcr0576c4q0smv6kxpv94gnrm3qzl6kvmaawd";
+          };
+          buildCommand = "gunzip < $src > $out";
         };
-        buildCommand = "gunzip < $src > $out";
-      };
-      gff3 = stage {
-        name = "ensembl-grch38-gff-${version}";
-        src = pkgs.fetchurl {
-          url =
-            "ftp://ftp.ensembl.org/pub/release-${version}/gff3/homo_sapiens/Homo_sapiens.GRCh38.${version}.gff3.gz";
-          sha256 = "1xvhsn938mw0032qgc9dvw3k2xrhpx77b8ms03fkrs2s67f7zli7";
+        gff3 = stage {
+          name = "ensembl-grch38-gff-${version}";
+          src = pkgs.fetchurl {
+            url =
+              "ftp://ftp.ensembl.org/pub/release-${version}/gff3/homo_sapiens/Homo_sapiens.GRCh38.${version}.gff3.gz";
+            sha256 = "1xvhsn938mw0032qgc9dvw3k2xrhpx77b8ms03fkrs2s67f7zli7";
+          };
+          buildCommand = "gunzip < $src > $out";
         };
-        buildCommand = "gunzip < $src > $out";
       };
-    };
     snpeff = {
       db = pkgs.stdenv.mkDerivation rec {
         name = "GRCh38.86";
@@ -221,48 +225,50 @@ rec {
       buildCommand = "gunzip < $src > $out";
       passthru.filetype = filetype.fa { };
     };
-    ensembl = let version = "94";
-    in {
-      cdna = stage {
-        name = "ensembl-grcm38-cdna-${version}";
-        src = pkgs.fetchurl {
-          url =
-            "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz";
-          sha256 = "0khp9l6s35lav2xqp7vkk6ybnz4wjihn7lapjf2lbpnbzjb4hp6d";
+    ensembl =
+      let version = "94";
+      in
+      {
+        cdna = stage {
+          name = "ensembl-grcm38-cdna-${version}";
+          src = pkgs.fetchurl {
+            url =
+              "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz";
+            sha256 = "0khp9l6s35lav2xqp7vkk6ybnz4wjihn7lapjf2lbpnbzjb4hp6d";
+          };
+          buildCommand = "gunzip < $src > $out";
+          passthru.filetype = filetype.fa { };
         };
-        buildCommand = "gunzip < $src > $out";
-        passthru.filetype = filetype.fa { };
-      };
-      ncrna = stage {
-        name = "ensembl-grcm38-ncrna-${version}";
-        version = "94";
-        src = pkgs.fetchurl {
-          url =
-            "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz";
-          sha256 = "0d997gm8p2b89rm5d46m2x4vz9lijxarfr2lzylnbi8gyqrbagdd";
+        ncrna = stage {
+          name = "ensembl-grcm38-ncrna-${version}";
+          version = "94";
+          src = pkgs.fetchurl {
+            url =
+              "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz";
+            sha256 = "0d997gm8p2b89rm5d46m2x4vz9lijxarfr2lzylnbi8gyqrbagdd";
+          };
+          buildCommand = "gunzip < $src > $out";
+          passthru.filetype = filetype.fa { };
         };
-        buildCommand = "gunzip < $src > $out";
-        passthru.filetype = filetype.fa { };
-      };
-      gtf = stage {
-        name = "ensembl-grcm38-gtf-${version}";
-        src = pkgs.fetchurl {
-          url =
-            "ftp://ftp.ensembl.org/pub/release-${version}/gtf/mus_musculus/Mus_musculus.GRCm38.${version}.gtf.gz";
-          sha256 = "0i61jq5i5bcini5nxqxxp3rnz2xzgychvzdn0k451f5rv053lp3v";
+        gtf = stage {
+          name = "ensembl-grcm38-gtf-${version}";
+          src = pkgs.fetchurl {
+            url =
+              "ftp://ftp.ensembl.org/pub/release-${version}/gtf/mus_musculus/Mus_musculus.GRCm38.${version}.gtf.gz";
+            sha256 = "0i61jq5i5bcini5nxqxxp3rnz2xzgychvzdn0k451f5rv053lp3v";
+          };
+          buildCommand = "gunzip < $src > $out";
         };
-        buildCommand = "gunzip < $src > $out";
-      };
-      gff3 = stage {
-        name = "ensembl-grcm38-gff-${version}";
-        src = pkgs.fetchurl {
-          url =
-            "ftp://ftp.ensembl.org/pub/release-${version}/gff3/mus_musculus/Mus_musculus.GRCm38.${version}.gff3.gz";
-          sha256 = "15fmdpx6g96fygwhs10jwrb2q5p9y64bc3d4clg856k57qzzgprg";
+        gff3 = stage {
+          name = "ensembl-grcm38-gff-${version}";
+          src = pkgs.fetchurl {
+            url =
+              "ftp://ftp.ensembl.org/pub/release-${version}/gff3/mus_musculus/Mus_musculus.GRCm38.${version}.gff3.gz";
+            sha256 = "15fmdpx6g96fygwhs10jwrb2q5p9y64bc3d4clg856k57qzzgprg";
+          };
+          buildCommand = "gunzip < $src > $out";
         };
-        buildCommand = "gunzip < $src > $out";
       };
-    };
   };
 
   mm10 = mm10-p4;
diff --git a/lib/shard-regex.nix b/lib/shard-regex.nix
index 06fba4d..9dc1720 100644
--- a/lib/shard-regex.nix
+++ b/lib/shard-regex.nix
@@ -1,54 +1,64 @@
-{bionix, n}:
+{ bionix, n }:
 
 with bionix;
 with lib.types;
 
 input:
 let
-  re = let f = matchFiletype' "shard-regex" {
+  re =
+    let f = matchFiletype' "shard-regex" {
       fa = _: "^>";
       fq = _: "^@";
       gz = f;
       bz2 = f;
     };
-  in f input.filetype;
-  decompress = matchFiletype "shard-regex-decompression" {
+    in f input.filetype;
+  decompress = matchFiletype "shard-regex-decompression"
+    {
       fa = _: "cat";
       fq = _: "cat";
       gz = _: "gunzip";
       bz2 = _: "bunzip2";
-    } input;
-  compress = matchFiletype "shard-regex-compression" {
+    }
+    input;
+  compress = matchFiletype "shard-regex-compression"
+    {
       fa = _: "cat";
       fq = _: "cat";
       gz = _: "gzip";
       bz2 = _: "bzip2";
-    } input;
-  compressPkgs = with bionix.pkgs; matchFiletype "shard-regex-compression" {
-      fa = _: [];
-      fq = _: [];
+    }
+    input;
+  compressPkgs = with bionix.pkgs; matchFiletype "shard-regex-compression"
+    {
+      fa = _: [ ];
+      fq = _: [ ];
       gz = _: [ gzip ];
       bz2 = _: [ bzip2 ];
-    } input;
-in stage {
+    }
+    input;
+in
+stage {
   name = "shard";
   outputs = [ "out" ] ++ builtins.genList (i: "out" + toString (i + 2)) (n - 1);
   buildInputs = [ pkgs.gawk ] ++ compressPkgs;
-  buildCommand = let
-    awkScript = pkgs.writeText "shard.awk" ''
-      BEGIN{cout=0}
-      FNR==NR{out[nout++] = $0;next}
-      /${re}/{cout = (cout + 1) % nout}
-      {print > out[cout]}
+  buildCommand =
+    let
+      awkScript = pkgs.writeText "shard.awk" ''
+        BEGIN{cout=0}
+        FNR==NR{out[nout++] = $0;next}
+        /${re}/{cout = (cout + 1) % nout}
+        {print > out[cout]}
+      '';
+    in
+    ''
+      for o in $outputs ; do
+        echo $(basename ''${!o}) >> outputs
+      done
+      awk -f ${awkScript} outputs <(${decompress} < ${input})
+      for o in $outputs ; do
+        ${compress} < $(basename ''${!o}) > ''${!o}
+      done
     '';
-  in ''
-    for o in $outputs ; do
-      echo $(basename ''${!o}) >> outputs
-    done
-    awk -f ${awkScript} outputs <(${decompress} < ${input})
-    for o in $outputs ; do
-      ${compress} < $(basename ''${!o}) > ''${!o}
-    done
-  '';
   passthru.filetype = input.filetype;
 }
diff --git a/lib/shard.nix b/lib/shard.nix
index 95cf251..9b85027 100644
--- a/lib/shard.nix
+++ b/lib/shard.nix
@@ -1,9 +1,9 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 with lib.types;
 
 {
-  regex = n: input: outputDrvs (callBionixE ./shard-regex.nix { n = n; } input);
-  fastQPair = n: {input1, input2}: lib.zipListsWith (i: j: {input1 = i; input2 = j;}) (lib.shard.regex n input1) (lib.shard.regex n input2);
+  regex = n: input: outputDrvs (callBionixE ./shard-regex.nix { inherit n; } input);
+  fastQPair = n: { input1, input2 }: lib.zipListsWith (i: j: { input1 = i; input2 = j; }) (lib.shard.regex n input1) (lib.shard.regex n input2);
 }
diff --git a/lib/slurm.nix b/lib/slurm.nix
index c050628..8c9ad50 100644
--- a/lib/slurm.nix
+++ b/lib/slurm.nix
@@ -4,23 +4,34 @@ with lib;
 
 let escape = x: if builtins.typeOf x == "string" then escapeShellArg x else x;
 
-in { ppn, mem, walltime, partition ? null, slurmFlags ? null
-, salloc ? "/usr/bin/salloc", srun ? "/usr/bin/srun", ... }:
+in
+{ ppn
+, mem
+, walltime
+, partition ? null
+, slurmFlags ? null
+, salloc ? "/usr/bin/salloc"
+, srun ? "/usr/bin/srun"
+, ...
+}:
 drv:
 let ppnReified = if drv.multicore then ppn else 1;
-in overrideDerivation drv ({ args, builder, name, ... }: {
+in
+overrideDerivation drv ({ args, builder, name, ... }: {
   builder = stdenv.shell;
-  args = let
-    slurm = writeScript "slurm" ''
-      #!${stdenv.shell}
-      NIX_BUILD_CORES=${toString ppnReified}
+  args =
+    let
+      slurm = writeScript "slurm" ''
+        #!${stdenv.shell}
+        NIX_BUILD_CORES=${toString ppnReified}
 
-      ${salloc} -c $NIX_BUILD_CORES --mem=${toString mem}G -t ${walltime} \
-        -J "${name}" \
-        ${optionalString (partition != null) "-p ${partition}"} \
-        ${optionalString (slurmFlags != null) slurmFlags} \
-        ${srun} ${builder} ${concatMapStringsSep " " escape args}
-    '';
+        ${salloc} -c $NIX_BUILD_CORES --mem=${toString mem}G -t ${walltime} \
+          -J "${name}" \
+          ${optionalString (partition != null) "-p ${partition}"} \
+          ${optionalString (slurmFlags != null) slurmFlags} \
+          ${srun} ${builder} ${concatMapStringsSep " " escape args}
+      '';
 
-  in [ "-c" slurm ];
+    in
+    [ "-c" slurm ];
 })
diff --git a/lib/types.nix b/lib/types.nix
index fbc7513..7e58ce0 100644
--- a/lib/types.nix
+++ b/lib/types.nix
@@ -1,4 +1,4 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 with lib;
@@ -25,30 +25,30 @@ rec {
   matchFiletype = sym: y: x: if x ? filetype then matchFiletype' sym y x.filetype else abort "unknown filetype for ${sym}";
   matchFiletype' = sym: y: x: match x (defError (idft sym) y filetype);
   filetype = make-type "filetype" {
-    fa = {};
-    fq = {};
-    bam = {ref = any; sorting = sort;};
-    sam = {ref = any; sorting = sort;};
-    cram = {ref = any; sorting = sort;};
-    vcf = {ref = any;};
-    bed = {ref = any;};
+    fa = { };
+    fq = { };
+    bam = { ref = any; sorting = sort; };
+    sam = { ref = any; sorting = sort; };
+    cram = { ref = any; sorting = sort; };
+    vcf = { ref = any; };
+    bed = { ref = any; };
     gz = filetype;
     bz2 = filetype;
   };
 
-  toCram = matchFiletype "bam2cram" { bam = filetype.cram; sam = filetype.cram; cram = filetype.cram; };
-  toBam = matchFiletype "bam2cram" { bam = filetype.bam; sam = filetype.bam; cram = filetype.bam; };
-  toSam = matchFiletype "bam2cram" { bam = filetype.sam; sam = filetype.sam; cram = filetype.sam; };
+  toCram = matchFiletype "bam2cram" { bam = filetype.cram; sam = filetype.cram; inherit (filetype) cram; };
+  toBam = matchFiletype "bam2cram" { inherit (filetype) bam; sam = filetype.bam; cram = filetype.bam; };
+  toSam = matchFiletype "bam2cram" { bam = filetype.sam; inherit (filetype) sam; cram = filetype.sam; };
 
   matchSorting = sym: y: x: match x.sorting (defError (idst sym) y sort);
   matchFileSorting = sym: y: let f = matchSorting sym y; in matchFiletype sym { bam = f; sam = f; cram = f; };
   sort = make-type "sort" {
-    none = {};
-    coord = {};
-    name = {};
+    none = { };
+    coord = { };
+    name = { };
   };
-  coordSort = f: matchFiletype "coordSort" { bam = x: filetype.bam (x // {sorting = sort.coord {};}); } {filetype = f;};
-  nameSort = f: matchFiletype "nameSort" { bam = x: filetype.bam (x // {sorting = sort.name {};}); } {filetype = f;};
+  coordSort = f: matchFiletype "coordSort" { bam = x: filetype.bam (x // { sorting = sort.coord { }; }); } { filetype = f; };
+  nameSort = f: matchFiletype "nameSort" { bam = x: filetype.bam (x // { sorting = sort.name { }; }); } { filetype = f; };
 
   gunzip = matchFiletype "gunzip" { gz = x: x; };
   bunzip2 = matchFiletype "bunzip2" { bz2 = x: x; };
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 6eb2e23..9ba0e51 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -1,4 +1,4 @@
-with import <bionix> {};
+with import <bionix> { };
 with lib;
 
 let
@@ -6,28 +6,32 @@ let
     name = baseNameOf path;
     buildCommand = "ln -s ${path} $out";
   };
-  fetchfq = attrs: types.tagFiletype (types.filetype.fq {}) (fetchlocal attrs);
-  fetchfa = attrs: types.tagFiletype (types.filetype.fa {}) (fetchlocal attrs);
+  fetchfq = attrs: types.tagFiletype (types.filetype.fq { }) (fetchlocal attrs);
+  fetchfa = attrs: types.tagFiletype (types.filetype.fa { }) (fetchlocal attrs);
 
   ref = fetchfa ./examples/ref.fa;
 
-  alignWithRG = rg: x: nameSort (bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";} x);
-  sort = samtools.sort {};
-  nameSort = samtools.sort {nameSort = true;};
-  flagstat = samtools.flagstat {};
-  check-fastqc = fastqc.check {};
-  check-fastp = fastp.check {};
-  callVariants = strelka.callSomatic {};
-  markdup = samtools.markdup {};
-  fixmate = samtools.fixmate {};
+  alignWithRG = rg: x: nameSort (bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'"; } x);
+  sort = sambamba.sort { };
+  nameSort = sambamba.sort { nameSort = true; };
+  flagstat = samtools.flagstat { };
+  check-fastqc = fastqc.check { };
+  check-fastp = fastp.check { };
+  callVariants = strelka.callSomatic { };
+  markdup = samtools.markdup { };
+  fixmate = samtools.fixmate { };
 
   tnpair = {
-    tumour = {name = "mysample1"; files = {
+    tumour = {
+      name = "mysample1";
+      files = {
         input1 = fetchfq ./examples/sample1-1.fq;
         input2 = fetchfq ./examples/sample1-2.fq;
       };
     };
-    normal = {name = "mysample2"; files = {
+    normal = {
+      name = "mysample2";
+      files = {
         input1 = fetchfq ./examples/sample2-1.fq;
         input2 = fetchfq ./examples/sample2-2.fq;
       };
@@ -37,36 +41,36 @@ let
   processPair = { tumour, normal }: rec {
     alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG x.name x.files)))) { inherit normal tumour; };
     variants = callVariants alignments;
-    octopusSomatic = octopus.callSomatic {} {inherit (alignments) normal; tumours = [ alignments.tumour ];};
-    glvariants = strelka.call {} (builtins.attrValues alignments);
-    platypusVars = platypus.call {} (builtins.attrValues alignments);
-    octopusVars = octopus.call {} (builtins.attrValues alignments);
-    shards = map (x: nameSort (bwa.align {inherit ref;} x)) (shard.fastQPair 2 normal.files);
+    octopusSomatic = octopus.callSomatic { } { inherit (alignments) normal; tumours = [ alignments.tumour ]; };
+    glvariants = strelka.call { } (builtins.attrValues alignments);
+    platypusVars = platypus.call { } (builtins.attrValues alignments);
+    octopusVars = octopus.call { } (builtins.attrValues alignments);
+    shards = map (x: nameSort (bwa.align { inherit ref; } x)) (shard.fastQPair 2 normal.files);
   };
 
   tnpairResult = processPair tnpair;
 
   cnvkitResults = rec {
-    cnvs = cnvkit.callCNV {} (with tnpairResult.alignments; { normals = [ normal ]; tumours = [ tumour ];});
-    plot = cnvkit.scatterPlot {} cnvs.out1;
+    cnvs = cnvkit.callCNV { } (with tnpairResult.alignments; { normals = [ normal ]; tumours = [ tumour ]; });
+    plot = cnvkit.scatterPlot { } cnvs.out1;
   };
 
   alignments = {
-    "bowtie-normal.bam" = bowtie.align {inherit ref;} tnpair.normal.files;
-    "last.maf" = lastal.align {inherit ref;} tnpair.normal.files;
-    "whisper.bam" = whisper.align {inherit ref;} tnpair.normal.files;
-    "bwa-mem.bam" = bwa.mem {inherit ref;} tnpair.normal.files;
-    "bwa-mem2.bam" = bwa.mem2 {inherit ref;} tnpair.normal.files;
-    "minimap2-normal.bam" = minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files;
-    "snap-normal.bam" = snap.align {inherit ref; } tnpair.normal.files;
+    "bowtie-normal.bam" = bowtie.align { inherit ref; } tnpair.normal.files;
+    "last.maf" = lastal.align { inherit ref; } tnpair.normal.files;
+    "whisper.bam" = whisper.align { inherit ref; } tnpair.normal.files;
+    "bwa-mem.bam" = bwa.mem { inherit ref; } tnpair.normal.files;
+    "bwa-mem2.bam" = bwa.mem2 { inherit ref; } tnpair.normal.files;
+    "minimap2-normal.bam" = minimap2.align { inherit ref; preset = "sr"; } tnpair.normal.files;
+    "snap-normal.bam" = snap.align { inherit ref; } tnpair.normal.files;
     "${tnpair.tumour.name}.flagstat" = flagstat tnpairResult.alignments.tumour;
-    "hisat2-normal.bam" = hisat2.align {inherit ref;} tnpair.normal.files;
+    "hisat2-normal.bam" = hisat2.align { inherit ref; } tnpair.normal.files;
   };
 
   testNaming = linkOutputs {
-    crai = samtools.index {} (samtools.view { outfmt = types.toCram; } tnpairResult.alignments.tumour);
-    kallisto = kallisto.quant {inherit ref;} (attrValues tnpair.tumour.files);
-    facets = facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];};
+    crai = samtools.index { } (samtools.view { outfmt = types.toCram; } tnpairResult.alignments.tumour);
+    kallisto = kallisto.quant { inherit ref; } (attrValues tnpair.tumour.files);
+    facets = facets.callCNV { } { vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ]; };
     cnvkit = cnvkitResults.cnvs;
     "cnvkit.pdf" = cnvkitResults.plot;
     "octopus.vcf" = tnpairResult.octopusVars;
@@ -74,24 +78,25 @@ let
     strelka-indels = tnpairResult.variants.indels;
     "strelka.snvs.vcf" = tnpairResult.variants.snvs;
     "strelka.gl.vcf" = tnpairResult.glvariants;
-    delly = delly.call {} (with tnpairResult.alignments; [normal tumour]);
-    lumpy = lumpy.call {} (with tnpairResult.alignments; [normal tumour]);
-    manta = manta.call {} (with tnpairResult.alignments; {normals = [normal tumour]; });
-    mantaTN = manta.call {} (with tnpairResult.alignments; {normals = [normal]; tumour = tumour;});
-    mantaT = manta.call {} (with tnpairResult.alignments; {tumour = tumour;});
-    gridss = gridss.callVariants {} (with tnpairResult.alignments; [normal tumour]);
-    gridss2 = gridss.call (with tnpairResult.alignments; [normal tumour]);
-    gridss3 = gridss.callAndAssemble (with tnpairResult.alignments; [normal tumour]);
-    "merged-shards.bam" = samtools.merge {} tnpairResult.shards;
-    "merged.bam" = samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal];
-    "merged-namesorted.bam" = samtools.merge {} [(nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal)];
-    "${tnpair.tumour.name}.cram" = samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour);
+    delly = delly.call { } (with tnpairResult.alignments; [ normal tumour ]);
+    lumpy = lumpy.call { } (with tnpairResult.alignments; [ normal tumour ]);
+    manta = manta.call { } (with tnpairResult.alignments; { normals = [ normal tumour ]; });
+    mantaTN = manta.call { } (with tnpairResult.alignments; { normals = [ normal ]; inherit tumour; });
+    mantaT = manta.call { } (with tnpairResult.alignments; { inherit tumour; });
+    gridss = gridss.callVariants { } (with tnpairResult.alignments; [ normal tumour ]);
+    gridss2 = gridss.call (with tnpairResult.alignments; [ normal tumour ]);
+    gridss3 = gridss.callAndAssemble (with tnpairResult.alignments; [ normal tumour ]);
+    "merged-shards.bam" = samtools.merge { } tnpairResult.shards;
+    "merged.bam" = samtools.merge { } [ tnpairResult.alignments.tumour tnpairResult.alignments.normal ];
+    "merged-namesorted.bam" = samtools.merge { } [ (nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal) ];
+    "${tnpair.tumour.name}.cram" = samtools.view { outfmt = types.toCram; } tnpairResult.alignments.tumour;
     "${tnpair.tumour.name}.fastqc.1" = check-fastqc tnpair.tumour.files.input1;
     "${tnpair.tumour.name}.fastp" = check-fastp tnpair.tumour.files;
-    snver = snver.call { ploidy=1; } tnpairResult.alignments;
-    mosdepth = mosdepth.plot {} { inputs = mapAttrsToList (_: mosdepth.depth {}) tnpairResult.alignments; names = [ "seq1" "seq2" ]; };
-    xenomapper = xenomapper.allocate {} { primary = nameSort tnpairResult.alignments.tumour; secondary = nameSort tnpairResult.alignments.tumour; };
+    snver = snver.call { ploidy = 1; } tnpairResult.alignments;
+    mosdepth = mosdepth.plot { } { inputs = mapAttrsToList (_: mosdepth.depth { }) tnpairResult.alignments; names = [ "seq1" "seq2" ]; };
+    xenomapper = xenomapper.allocate { } { primary = nameSort tnpairResult.alignments.tumour; secondary = nameSort tnpairResult.alignments.tumour; };
     inherit alignments;
   };
 
-in testNaming
+in
+testNaming
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
+}