From bac9248a5e08e8afdf5485a6e27cfe72e1ca5090 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 29 Oct 2021 17:39:01 +1100
Subject: treewide reformatting and simplification

- simplify with statix
- reformat with nixpkgs-fmt
---
 tools/bwa-mem2.nix | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'tools/bwa-mem2.nix')

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;
 }
-- 
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