treewide reformatting and simplification

- simplify with statix
- reformat with nixpkgs-fmt

3 files changed, 29 insertions, 21 deletions

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;