treewide reformatting and simplification

- simplify with statix
- reformat with nixpkgs-fmt

87 files changed, 524 insertions, 458 deletions

diff --git a/tools/ascat-app.nix b/tools/ascat-app.nix
index 51aa677..bd6d538 100644
--- a/tools/ascat-app.nix
+++ b/tools/ascat-app.nix
@@ -1,4 +1,4 @@
-{stdenv, callPackage, buildPerlPackage, fetchurl, fetchFromGitHub, perlPackages, R, bwa, samtools, pkgconfig, zlib, htslib, curl, bzip2, lzma, gnutls, nettle, gmp, p11-kit, libtasn1, perl, psmisc, time, vcftools, rWrapper, rPackages}:
+{ stdenv, callPackage, buildPerlPackage, fetchurl, fetchFromGitHub, perlPackages, R, bwa, samtools, pkgconfig, zlib, htslib, curl, bzip2, lzma, gnutls, nettle, gmp, p11-kit, libtasn1, perl, psmisc, time, vcftools, rWrapper, rPackages }:
 
 let
   ascat = fetchurl {
@@ -98,7 +98,7 @@ let
       url = "mirror://cpan/authors/id/C/CD/CDRAUG/${name}.tar.gz";
       sha256 = "0yvhgifs8g9rwdcq84zw4b005nq2jml6c75zgjscv6d2pd3lj1ss";
     };
-    propagatedBuildInputs = with perlPackages; [DBI DataStag Error GD Graph HTTPMessage HTTPMessage IOstringy IOString IPCRun LWP ListMoreUtils SetScalar TestMost TestRequiresInternet URI XMLDOM XMLDOMXPath XMLLibXML XMLLibXML libxml_perl XMLSAX XMLSAXBase XMLSAXWriter XMLTwig XMLWriter YAML DBFile ];
+    propagatedBuildInputs = with perlPackages; [ DBI DataStag Error GD Graph HTTPMessage HTTPMessage IOstringy IOString IPCRun LWP ListMoreUtils SetScalar TestMost TestRequiresInternet URI XMLDOM XMLDOMXPath XMLLibXML XMLLibXML libxml_perl XMLSAX XMLSAXBase XMLSAXWriter XMLTwig XMLWriter YAML DBFile ];
     nativeBuildInputs = with perlPackages; [ TestException TestWarn TestDifferences TestDeep ];
   };
 
@@ -108,7 +108,7 @@ let
       url = "mirror://cpan/authors/id/C/CM/CMUNGALL/${name}.tar.gz";
       sha256 = "0ncf4l39ka23nb01jlm6rzxdb5pqbip01x0m38bnvf1gim825caa";
     };
-    propagatedBuildInputs = with perlPackages; [IOString Graph XMLLibXSLT ];
+    propagatedBuildInputs = with perlPackages; [ IOString Graph XMLLibXSLT ];
   };
 
   XMLDOMXPath = buildPerlPackage rec {
@@ -117,7 +117,7 @@ let
       url = "mirror://cpan/authors/id/M/MI/MIROD/${name}.tar.gz";
       sha256 = "1si9m1pqih3ibbd6jnw69fh98dd4krxpx90p65x9j4aja55afwq1";
     };
-    propagatedBuildInputs= with perlPackages; [XMLDOM XMLXPathEngine];
+    propagatedBuildInputs = with perlPackages; [ XMLDOM XMLXPathEngine ];
     doCheck = false;
   };
 
@@ -215,10 +215,10 @@ let
     name = "alleleCount.pl-${version}";
     version = "4.0.1";
     src = fetchFromGitHub {
-    owner = "cancerit";
-    repo = "alleleCount";
-    rev = "v${version}";
-    sha256 = "0nkwnjqglgshzhlmz1r0khdjai9mfz4ih8bzrzg0g18d1725k6gp";
+      owner = "cancerit";
+      repo = "alleleCount";
+      rev = "v${version}";
+      sha256 = "0nkwnjqglgshzhlmz1r0khdjai9mfz4ih8bzrzg0g18d1725k6gp";
     };
     preConfigure = ''
       cd perl
@@ -266,4 +266,5 @@ let
     ];
   };
 
-in ascatNGS
+in
+ascatNGS
diff --git a/tools/ascat-callCNV.nix b/tools/ascat-callCNV.nix
index f74bb18..aa1a8ec 100644
--- a/tools/ascat-callCNV.nix
+++ b/tools/ascat-callCNV.nix
@@ -1,12 +1,12 @@
 { bionix
 , ref
 , gc
-, indexAttrs ? {}
-, bamIndexAttrs ? {}
+, indexAttrs ? { }
+, bamIndexAttrs ? { }
 , flags ? null
 }:
 
-{tumour, normal, gender}:
+{ tumour, normal, gender }:
 
 with bionix;
 with lib;
diff --git a/tools/ascat.nix b/tools/ascat.nix
index 700cb4e..142e0d9 100644
--- a/tools/ascat.nix
+++ b/tools/ascat.nix
@@ -1,17 +1,17 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
 {
-  app = pkgs.callPackage ./ascat-app.nix {};
+  app = pkgs.callPackage ./ascat-app.nix { };
 
   /* Generate GC correction file for ascatNGS.
-  Type: gccorrect :: {ref :: fasta, chrPrefix :: string, ...} -> (snps :: VCF) -> (gc :: GC)
+    Type: gccorrect :: {ref :: fasta, chrPrefix :: string, ...} -> (snps :: VCF) -> (gc :: GC)
   */
   gccorrect = callBionixE ./ascat-gccorrect.nix;
 
   /* Call CNVs using ascatNGS. Gender is a string as per ascatNGS docs (e.g., "XX").
-  Type: callCNV :: {ref :: fasta, gc :: GC, ...} -> {tumour :: bam, normal :: bam, gender :: string} -> CNVs
+    Type: callCNV :: {ref :: fasta, gc :: GC, ...} -> {tumour :: bam, normal :: bam, gender :: string} -> CNVs
   */
   callCNV = callBionixE ./ascat-callCNV.nix;
 }
diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix
index c83c49c..8df3dba 100644
--- a/tools/bowtie-align.nix
+++ b/tools/bowtie-align.nix
@@ -2,7 +2,7 @@
 , ref
 , bamOutput ? true
 , flags ? null
-, indexAttrs ? {}
+, indexAttrs ? { }
 }:
 
 { input1
@@ -18,7 +18,8 @@ let
   fa = f: matchFiletype "bowtie2-ref" { fa = _: f; } f;
   fq = f: matchFiletype "bowtie2-input" { fq = _: f; gz = matchFiletype' "bowtie2-input" { fq = _: f; }; } f;
 
-in stage {
+in
+stage {
   name = "bowtie2-align";
   buildInputs = with pkgs; [ bowtie2 bc samtools ];
   buildCommand = ''
@@ -32,6 +33,6 @@ 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;
 }
diff --git a/tools/bowtie.nix b/tools/bowtie.nix
index df97d36..2208dff 100644
--- a/tools/bowtie.nix
+++ b/tools/bowtie.nix
@@ -4,12 +4,12 @@ with bionix;
 
 {
   /* Align a sequence against a reference
-  Type: align :: {ref :: fasta, bamOutput :: bool, ...} -> {input1 :: fastq, input2 :: fastq} -> bam/sam
+    Type: align :: {ref :: fasta, bamOutput :: bool, ...} -> {input1 :: fastq, input2 :: fastq} -> bam/sam
   */
   align = callBionixE ./bowtie-align.nix;
 
   /* Create a Bowtie index
-  Type: index :: {seed :: int, ...} -> fasta -> index
+    Type: index :: {seed :: int, ...} -> fasta -> index
   */
   index = callBionixE ./bowtie-index.nix;
 }
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 31c9487..52e73d1 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.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-mem";
   buildInputs = with pkgs; [ bwa 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;
 }
diff --git a/tools/bwa-mem2-app.nix b/tools/bwa-mem2-app.nix
index 49f4af3..6ee2ab4 100644
--- a/tools/bwa-mem2-app.nix
+++ b/tools/bwa-mem2-app.nix
@@ -1,5 +1,5 @@
 { clangStdenv, fetchFromGitHub, zlib }:
-  clangStdenv.mkDerivation rec {
+clangStdenv.mkDerivation rec {
   pname = "bwa-mem2";
   version = "2.1";
   src = fetchFromGitHub {
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;
 }
diff --git a/tools/bwa.nix b/tools/bwa.nix
index 90a8bd3..6fb7d71 100644
--- a/tools/bwa.nix
+++ b/tools/bwa.nix
@@ -3,18 +3,18 @@
 with bionix;
 
 rec {
-  app2 = pkgs.callPackage ./bwa-mem2-app.nix {};
+  app2 = pkgs.callPackage ./bwa-mem2-app.nix { };
 
   /* Align read against a reference: defaults to bwa-mem */
   align = bionix.bwa.mem;
 
   /* Align reads against a reference using bwa-mem
-  Type: bwa-mem :: {ref :: fasta, bamOutput :: bool, ...} -> {input1, input2} -> bam/sam
+    Type: bwa-mem :: {ref :: fasta, bamOutput :: bool, ...} -> {input1, input2} -> bam/sam
   */
   mem = callBionixE ./bwa-mem.nix;
   mem2 = callBionixE ./bwa-mem2.nix;
   /* Creates an reference index for BWA
-  Type: index :: {...} -> fasta -> BWA index
+    Type: index :: {...} -> fasta -> BWA index
   */
   index = callBionixE ./bwa-index.nix;
   index2 = callBionixE ./bwa-index2.nix;
diff --git a/tools/cnvkit-batch.nix b/tools/cnvkit-batch.nix
index 113e0c9..7f7893f 100644
--- a/tools/cnvkit-batch.nix
+++ b/tools/cnvkit-batch.nix
@@ -1,17 +1,18 @@
-{bionix
-,targets ? null
-,annotations ? null
-,flags ? null
-,indexAttrs ? {}}:
+{ bionix
+, targets ? null
+, annotations ? null
+, flags ? null
+, indexAttrs ? { }
+}:
 
-{normals ? [], tumours}:
+{ normals ? [ ], tumours }:
 
 with bionix;
 with lib;
 with types;
 
 let
-  getref = f: matchFiletype "cnvkit-batch" { bam = {ref, ...}: ref; } f;
+  getref = matchFiletype "cnvkit-batch" { bam = { ref, ... }: ref; };
   refs = map getref normals ++ map getref tumours;
   ref = head refs;
   sorted = matchFileSorting "cnvkit-batch" { coord = _: true; };
diff --git a/tools/cnvkit-scatter.nix b/tools/cnvkit-scatter.nix
index 2899584..6cd5b96 100644
--- a/tools/cnvkit-scatter.nix
+++ b/tools/cnvkit-scatter.nix
@@ -1,5 +1,6 @@
-{bionix
-,flags ? null}:
+{ bionix
+, flags ? null
+}:
 
 input:
 
diff --git a/tools/cnvkit.nix b/tools/cnvkit.nix
index fc55d94..812652a 100644
--- a/tools/cnvkit.nix
+++ b/tools/cnvkit.nix
@@ -1,15 +1,15 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
 {
   /* Call CNVs
-  Type: callCNV :: {targets :: target file, annotations :: annotation file, ...} -> {normals :: [bam], tumours :: [bam]} -> CNVs
+    Type: callCNV :: {targets :: target file, annotations :: annotation file, ...} -> {normals :: [bam], tumours :: [bam]} -> CNVs
   */
   callCNV = callBionixE ./cnvkit-batch.nix;
 
   /* Scatter plot from CNV calls
-  Type: scatterPlot :: {} -> CNVs -> PDF
+    Type: scatterPlot :: {} -> CNVs -> PDF
   */
   scatterPlot = callBionixE ./cnvkit-scatter.nix;
 }
diff --git a/tools/compression-bunzip2.nix b/tools/compression-bunzip2.nix
index 06fe682..a36b66d 100644
--- a/tools/compression-bunzip2.nix
+++ b/tools/compression-bunzip2.nix
@@ -1,4 +1,4 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
diff --git a/tools/compression-bzip2.nix b/tools/compression-bzip2.nix
index 6dfb749..5332e7d 100644
--- a/tools/compression-bzip2.nix
+++ b/tools/compression-bzip2.nix
@@ -1,4 +1,4 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
diff --git a/tools/compression-gunzip.nix b/tools/compression-gunzip.nix
index 6c98f91..96a4e49 100644
--- a/tools/compression-gunzip.nix
+++ b/tools/compression-gunzip.nix
@@ -1,4 +1,4 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
diff --git a/tools/compression-gzip.nix b/tools/compression-gzip.nix
index 50fca9e..0229b94 100644
--- a/tools/compression-gzip.nix
+++ b/tools/compression-gzip.nix
@@ -1,4 +1,4 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 
diff --git a/tools/compression.nix b/tools/compression.nix
index bfcc292..c9c8777 100644
--- a/tools/compression.nix
+++ b/tools/compression.nix
@@ -1,4 +1,4 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 with types;
@@ -8,42 +8,51 @@ let
   gunzip = callBionixE ./compression-gunzip.nix;
   bunzip2 = callBionixE ./compression-bunzip2.nix;
 
-in {
-  uncompress = attrs: f: matchFiletype "uncompress" {
-    fa = _: f;
-    fq = _: f;
-    bam = _: f;
-    sam = _: f;
-    cram = _: f;
-    vcf = _: f;
-    bed = _: f;
-    gz = _: gunzip attrs f;
-    bz2 = _: bunzip2 attrs f;
-  } f;
+in
+{
+  uncompress = attrs: f: matchFiletype "uncompress"
+    {
+      fa = _: f;
+      fq = _: f;
+      bam = _: f;
+      sam = _: f;
+      cram = _: f;
+      vcf = _: f;
+      bed = _: f;
+      gz = _: gunzip attrs f;
+      bz2 = _: bunzip2 attrs f;
+    }
+    f;
 
   gzip