treewide reformatting and simplification

- simplify with statix
- reformat with nixpkgs-fmt

7 files changed, 51 insertions, 37 deletions

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)