treewide reformatting and simplification

- simplify with statix
- reformat with nixpkgs-fmt

7 files changed, 259 insertions, 219 deletions

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; };