treewide reformatting and simplification

- simplify with statix
- reformat with nixpkgs-fmt

104 files changed, 936 insertions, 802 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;