From 871ef64f3c43199dfa01216ac86db56650c2c8a2 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 5 Oct 2018 16:16:20 +1000
Subject: implement types

---
 default.nix                     |  4 +++
 lib/references.nix              |  5 ++++
 lib/types.nix                   | 64 +++++++++++++++++++++++++++++++++++++++++
 test-tnpair.nix                 | 31 +++++++++++++++-----
 tools/bwa-index.nix             |  5 +++-
 tools/bwa-mem.nix               | 15 +++++++---
 tools/compression.nix           | 58 +++++++++++++++++++++++++++++++++++++
 tools/crumble-toCram.nix        | 15 ----------
 tools/crumble.nix               |  1 -
 tools/gridss-callVariants.nix   | 13 +++++++--
 tools/gridss.nix                |  2 +-
 tools/platypus-callVariants.nix | 20 +++++++++----
 tools/platypus.nix              |  4 +--
 tools/samtools-faidx.nix        |  3 ++
 tools/samtools-index.nix        |  4 +++
 tools/samtools-sort.nix         | 15 ++++++++--
 tools/samtools-view.nix         | 27 +++++++++++++++++
 tools/samtools.nix              |  1 +
 tools/strelka-call.nix          | 15 +++++++---
 19 files changed, 258 insertions(+), 44 deletions(-)
 create mode 100644 lib/types.nix
 create mode 100644 tools/compression.nix
 delete mode 100644 tools/crumble-toCram.nix
 create mode 100644 tools/samtools-view.nix

diff --git a/default.nix b/default.nix
index 1a8f341..7002a57 100644
--- a/default.nix
+++ b/default.nix
@@ -7,7 +7,10 @@ let
       callBionix = callBionix;
       id = x: x;
 
+      types = callBionix ./lib/types.nix {};
+
       bwa = callBionix ./tools/bwa.nix {};
+      compression = callBionix ./tools/compression.nix {};
       crumble = callBionix ./tools/crumble.nix {};
       fastqc = callBionix ./tools/fastqc.nix {};
       gridss = callBionix ./tools/gridss.nix {};
@@ -22,5 +25,6 @@ let
       ref = callBionix ./lib/references.nix {};
       def = f: defs: attrs: f (defs // attrs);
       defQsub = qsubAttrs: f: defs: qsubAttr qsubAttrs (def f defs);
+
   });
 in bionix
diff --git a/lib/references.nix b/lib/references.nix
index 61655cd..3614647 100755
--- a/lib/references.nix
+++ b/lib/references.nix
@@ -1,6 +1,7 @@
 { bionix, nixpkgs }:
 
 with nixpkgs;
+with bionix.types;
 
 rec {
   grch38 = grch38-p12;
@@ -13,6 +14,7 @@ rec {
         sha256 = "0ji2ggpmgnbpwbhq8mirj6h3lyy02nl2rnz7n892iq5cqpsblh4z";
       };
       buildCommand = "gunzip < $src > $out";
+      passthru.filetype = filetype.fa {};
     };
     blacklist = stdenvNoCC.mkDerivation {
       name = "blacklist-grch38";
@@ -21,6 +23,7 @@ rec {
         sha256 = "1lpnqq1mjidbdxj5i6x26rxa8x1rs8q3hlf0z1z49j3jsnkgffky";
       };
       buildCommand = "gunzip < $src > $out";
+      passthru.filetype = filetype.bed { ref = seq; };
     };
   };
 
@@ -34,6 +37,7 @@ rec {
         sha256 = "0ryiqab5bldpzawylsk2qpjxr2j701q03ww9jqyxhkimqpn9g3mr";
       };
       buildCommand = "gunzip < $src > $out";
+      passthru.filetype = filetype.fa {};
     };
   };
 
@@ -47,6 +51,7 @@ rec {
               sha256 = "1660d6d05f3aa266c6053cfd1efef1747d9e854836917241d6f47cff7a55340c";
               };
           buildCommand = "gunzip < $src > $out";
+          passthru.filetype = filetype.fa {};
       };
   };
 }
diff --git a/lib/types.nix b/lib/types.nix
new file mode 100644
index 0000000..a347046
--- /dev/null
+++ b/lib/types.nix
@@ -0,0 +1,64 @@
+{bionix, nixpkgs}:
+
+with nixpkgs;
+
+let
+  nix-adt-src = fetchFromGitHub {
+    owner = "shlevy";
+    repo = "nix-adt";
+    rev = "dd04b5d08eed65ecd73aafde56a78078e09f1c74";
+    sha256 = "0vhk1y7gilgn2pgvj4813bh2ljpw4pvrph8k8b0fsg56dbm8mqxa";
+  };
+  nix-adt = import "${nix-adt-src}";
+  inherit (nix-adt.checked) make-type match any std none;
+  inherit (std) option;
+
+  idft = sym: ft: _: abort "unhandled filetype (${ft}) for ${sym}";
+  idst = sym: st: _: abort "unhandled sorting (${st}) for ${sym}";
+
+in
+rec {
+  option-sort = option sorting;
+
+  matchFiletype = sym: y: x: if x ? filetype then match x.filetype ({
+    fa = idft sym "fasta";
+    fq = idft sym "fastq";
+    bam = idft sym "bam";
+    sam = idft sym "sam";
+    cram = idft sym "cram";
+    vcf = idft sym "vcf";
+    bed = idft sym "bed";
+    gz = idft sym "gz";
+    bz2 = idft sym "bz2";
+  } // y) else abort "unknown filetype for ${sym}";
+  filetype = make-type "filetype" {
+    fa = {};
+    fq = {};
+    bam = {ref = any; sorting = option-sort;};
+    sam = {ref = any; sorting = option-sort;};
+    cram = {ref = any; sorting = option-sort;};
+    vcf = {ref = any;};
+    bed = {ref = any;};
+    gz = filetype;
+    bz2 = filetype;
+  };
+
+  toCram = matchFiletype "bam2cram" { bam = filetype.cram; sam = filetype.cram; cram = filetype.cram; };
+  toBam = matchFiletype "bam2cram" { bam = filetype.bam; sam = filetype.bam; cram = filetype.bam; };
+  toSam = matchFiletype "bam2cram" { bam = filetype.sam; sam = filetype.sam; cram = filetype.sam; };
+
+  matchSorting = sym: y: let f = x: match x.sorting { some = z: match z ( { coord = idst sym "coord"; name = idst sym "name"; } // y); none = abort "unknown sort for ${sym}"; }; in matchFiletype sym { bam = f; sam = f; cram = f; };
+  sorting = make-type "sorting" {
+    coord = {};
+    name = {};
+  };
+  coordSort = f: matchFiletype "coordSort" { bam = x: filetype.bam (x // {sorting = option-sort.some (sorting.coord {});}); } {filetype = f;};
+  nameSort = f: matchFiletype "nameSort" { bam = x: filetype.bam (x // {sorting = option-sort.some (sorting.name {});}); } {filetype = f;};
+
+  gunzip = matchFiletype "gunzip" { gz = x: x; };
+  bunzip2 = matchFiletype "bunzip2" { bz2 = x: x; };
+
+  tag = attrs: x: if x ? type && x.type == "derivation" then x // attrs else tagPassthru attrs x;
+  tagPassthru = attrs: x: if x ? passthru then x // { passthru = x.passthru // attrs; } else x // { passthru = attrs; };
+  tagFiletype = ft: tag { filetype = ft; };
+}
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 3260b7b..7deaf3b 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -14,15 +14,31 @@ in
 with bionix;
 
 let
-  ref = { seq = ./example/ref.fa; };
-  alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
+  fetchlocal = path: stdenv.mkDerivation {
+    name = baseNameOf path;
+    buildCommand = "ln -s ${path} $out";
+  };
+  fetchfq = attrs: types.tagFiletype (types.filetype.fq {}) (fetchlocal attrs);
+  fetchfa = attrs: types.tagFiletype (types.filetype.fa {}) (fetchlocal attrs);
+
+  alignWithRG = rg: bwa.align { ref = fetchfa ./example/ref.fa; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
   sort = samtools.sort {};
   flagstat = samtools.flagstat {};
   check = fastqc.check {};
-  callVariants = strelka.call { inherit ref; };
+  callVariants = strelka.call {};
 
-  tnpair = { tumour = {name = "mysample1"; files = {input1 = ./example/sample1-1.fq; input2 = ./example/sample1-2.fq;};};
-             normal = {name = "mysample2"; files = {input1 = ./example/sample2-1.fq; input2 = ./example/sample2-1.fq;};};};
+  tnpair = {
+    tumour = {name = "mysample1"; files = {
+        input1 = fetchfq ./example/sample1-1.fq;
+        input2 = fetchfq ./example/sample1-2.fq;
+      };
+    };
+    normal = {name = "mysample2"; files = {
+        input1 = fetchfq ./example/sample2-1.fq;
+        input2 = fetchfq ./example/sample2-1.fq;
+      };
+    };
+  };
 
   processPair = { tumour, normal }: rec {
     alignments = mapAttrs (_: x: sort (alignWithRG x.name x.files)) { inherit normal tumour; };
@@ -37,8 +53,9 @@ let
       mkdir $out
       ln -s ${tnpairResult.variants} $out/strelka
       mkdir $out/alignments
-      ln -s ${tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.bam
-      ln -s ${tnpairResult.alignments.normal} $out/alignments/${tnpair.normal.name}.bam
+      ln -s ${gridss.callVariants {} (with tnpairResult.alignments; [tumour])} $out/gridss
+      ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)} $out/alignments/${tnpair.tumour.name}.cram
+      ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)} $out/alignments/${tnpair.normal.name}.cram
       ln -s ${flagstat tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.flagstat
       ln -s ${flagstat tnpairResult.alignments.normal} $out/alignments/${tnpair.normal.name}.flagstat
       mkdir $out/fastqc
diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix
index 48a2556..c879bc4 100644
--- a/tools/bwa-index.nix
+++ b/tools/bwa-index.nix
@@ -7,12 +7,15 @@ ref:
 
 with nixpkgs;
 with lib;
+with bionix.types;
+
+assert (matchFiletype "bwa-index" { fa = _: true; } ref);
 
 stdenv.mkDerivation {
   name = "bwa-index";
   buildInputs = [ bwa ];
   buildCommand = ''
-    ln -s ${ref.seq} ref.fa
+    ln -s ${ref} ref.fa
     bwa index ${optionalString (flags != null) flags} ref.fa
     mkdir $out
     mv ref.fa.* $out
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index ca9e6a8..0d0f7d8 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -12,12 +12,18 @@
 
 with nixpkgs;
 with lib;
+with bionix.types;
+with bionix.compression;
 
-stdenv.mkDerivation {
+let
+  fa = f: matchFiletype "bwa-ref" { fa = _: f; } f;
+  fq = f: matchFiletype "bwa-input" { fq = _: f; } f;
+
+in stdenv.mkDerivation {
   name = "bwa-mem";
   buildInputs = [ bwa bc ] ++ optional bamOutput samtools;
   buildCommand = ''
-    ln -s ${ref.seq} ref.fa
+    ln -s ${fa ref} ref.fa
     for f in ${bionix.bwa.index indexAttrs ref}/* ; do
       ln -s $f
     done
@@ -26,9 +32,10 @@ stdenv.mkDerivation {
       >&2 echo "not enough build cores"
       exit 1
     fi
-    bwa mem ${optionalString (flags != null) flags} -t $cores ref.fa ${input1} \
-      ${optionalString (input2 != null) input2} \
+    bwa mem ${optionalString (flags != null) flags} -t $cores ref.fa ${fq input1} \
+      ${optionalString (input2 != null) (fq input2)} \
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = option-sort.none;} else filetype.sam {ref = ref; sorting = option-sort.none;};
 }
diff --git a/tools/compression.nix b/tools/compression.nix
new file mode 100644
index 0000000..aea7e13
--- /dev/null
+++ b/tools/compression.nix
@@ -0,0 +1,58 @@
+{bionix, nixpkgs}:
+
+with nixpkgs;
+with bionix;
+
+{
+  uncompress = f: types.matchFiletype "uncompress" {
+    fa = _: f;
+    fq = _: f;
+    bam = _: f;
+    sam = _: f;
+    cram = _: f;
+    vcf = _: f;
+    bed = _: f;
+    gz = _: types.tagFiletype (types.gunzip f.filetype) (stdenv.mkDerivation {
+      name = "gunzip";
+      buildCommand = "gunzip < ${f} > $out";
+    });
+    bz2 = _: types.tagFiletype (types.bunzip2 f.filetype) (stdenv.mkDerivation {
+      name = "bunzip2";
+      buildCommand = "bunzip2 < ${f} > $out";
+    });
+  } f.filetype;
+
+  gzip = f:
+    let
+      gz = (stdenv.mkDerivation {
+        name = "gzip";
+        buildCommand = "gzip < ${f} > $out";
+        passthru = { filetype = types.filetype.gz f.filetype; };
+      });
+    in types.matchFiletype "compressed" {
+      fa = _: gz;
+      fq = _: gz;
+      bam = _: gz;
+      sam = _: gz;
+      cram = _: gz;
+      vcf = _: gz;
+      bed = _: gz;
+    } f;
+
+  bzip2 = f:
+    let
+      bz2 = (stdenv.mkDerivation {
+        name = "bzip2";
+        buildCommand = "bzip2 < ${f} > $out";
+        passthru = { filetype = types.filetype.bz2 f.filetype; };
+      });
+    in types.matchFiletype "compressed" {
+      fa = _: gz;
+      fq = _: gz;
+      bam = _: gz;
+      sam = _: gz;
+      cram = _: gz;
+      vcf = _: gz;
+      bed = _: gz;
+    } f;
+}
diff --git a/tools/crumble-toCram.nix b/tools/crumble-toCram.nix
deleted file mode 100644
index 2544e17..0000000
--- a/tools/crumble-toCram.nix
+++ /dev/null
@@ -1,15 +0,0 @@
-{ bionix
-, nixpkgs
-, flags ? null
-}:
-
-with nixpkgs;
-with lib;
-
-input:
-
-stdenv.mkDerivation {
-  name = "crumble";
-  buildInputs = [ bionix.crumble.crumble ];
-  buildCommand = "crumble ${optionalString (flags != null) flags} ${input} $out";
-}
diff --git a/tools/crumble.nix b/tools/crumble.nix
index fb48c8f..6031fca 100644
--- a/tools/crumble.nix
+++ b/tools/crumble.nix
@@ -5,5 +5,4 @@ with bionix;
 
 {
   crumble = callPackage ./crumble-app.nix {};
-  toCram = callBionix ./crumble-toCram.nix;
 }
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index c313c3f..799c930 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -1,16 +1,25 @@
 { bionix
 , nixpkgs
-, ref
 , blacklist ? null
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
 , flags ? null
 }:
 
+with nixpkgs;
 with lib;
+with bionix.types;
 
 inputs:
 
+let
+  getref = matchFiletype "gridss-callVariants" { bam = x: x.ref; };
+  refs = map getref inputs;
+  ref = head refs;
+in
+
+assert (length (unique refs) == 1);
+
 stdenv.mkDerivation rec {
   name = "gridss-callVariants";
   buildInputs = [ jre R bwa ];
@@ -19,7 +28,7 @@ stdenv.mkDerivation rec {
     sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k";
   };
   buildCommand = ''
-    ln -s ${ref.seq} ref.fa
+    ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
     for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
       ln -s $f
diff --git a/tools/gridss.nix b/tools/gridss.nix
index edf9f57..7a2f217 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -3,5 +3,5 @@
 with bionix;
 
 {
-  callVariants = callBiolnix ./gridss-callVariants.nix;
+  callVariants = callBionix ./gridss-callVariants.nix;
 }
diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
index 7b68b28..a3e3a65 100644
--- a/tools/platypus-callVariants.nix
+++ b/tools/platypus-callVariants.nix
@@ -1,6 +1,5 @@
 { bionix
 , nixpkgs
-, ref
 , indexAttrs ? {}
 , bamIndexAttrs ? {}
 , flags ? null
@@ -8,16 +7,26 @@
 
 inputs:
 
+with nixpkgs;
 with lib;
+with bionix.types;
 
-let filename = path: last (splitString "/" path);
 
-in stdenv.mkDerivation {
+let
+  filename = path: last (splitString "/" path);
+  getref = f: matchFiletype "platypus-callVariants" { bam = r: r; } f;
+  refs = map getref inputs;
+  ref = head refs;
+in
+
+assert (length (unique refs) == 1);
+
+stdenv.mkDerivation {
   name = "platypus";
   buildInputs = [ platypus ];
   buildCommand = ''
-    ln -s ${ref.seq} ref.fa
-    ln -s ${bionix.samtools.faix indexAttrs ref} ref.fa.fai
+    ln -s ${ref} ref.fa
+    ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
     ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
     ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
     ls -l
@@ -28,4 +37,5 @@ in stdenv.mkDerivation {
       -o $out \
       --bamFiles=${concatMapStringsSep "," (p: "${filename p}.bam") inputs}
   '';
+  passthru.filetype = filetype.vcf {ref = ref;};
 }
diff --git a/tools/platypus.nix b/tools/platypus.nix
index 88d88d7..0dfe397 100644
--- a/tools/platypus.nix
+++ b/tools/platypus.nix
@@ -1,7 +1,7 @@
 { bionix, nixpkgs }:
 
-with nixpkgs;
+with bionix;
 
 {
-  call = attrs: callPackage ./platypus-callVariants.nix attrs;
+  call = callBionix ./platypus-callVariants.nix;
 }
diff --git a/tools/samtools-faidx.nix b/tools/samtools-faidx.nix
index bf32bdf..1fde411 100644
--- a/tools/samtools-faidx.nix
+++ b/tools/samtools-faidx.nix
@@ -7,6 +7,9 @@ input:
 
 with nixpkgs;
 with lib;
+with bionix.types;
+
+assert (matchFiletype "samtools-faidx" { fa = _: true; } input);
 
 stdenv.mkDerivation {
 
diff --git a/tools/samtools-index.nix b/tools/samtools-index.nix
index 4e09dc7..aad46a7 100644
--- a/tools/samtools-index.nix
+++ b/tools/samtools-index.nix
@@ -7,6 +7,10 @@ input:
 
 with nixpkgs;
 with lib;
+with bionix.types;
+
+assert (matchFiletype "samtools-index" { bam = _: true; } input);
+assert (matchSorting "samtools-index" { coord = _: true; } input);
 
 stdenv.mkDerivation {
   name = "samtools-index";
diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix
index 2de579e..ab9d603 100644
--- a/tools/samtools-sort.nix
+++ b/tools/samtools-sort.nix
@@ -2,6 +2,7 @@
 , nixpkgs
 , nameSort ? false
 , flags ? null
+, outfmt ? null
 }:
 
 input:
@@ -9,10 +10,20 @@ input:
 with nixpkgs;
 with lib;
 
-stdenv.mkDerivation {
+let
+  inherit (bionix.types) matchFiletype coordSort;
+in
+
+assert (matchFiletype "samtools-sort" { bam = _: true; sam = _: true; cram = _: true; } input);
+
+let
+  outfmtR = if outfmt != null then outfmt input else input.filetype;
+  outFmtFlags = matchFiletype "samtools-sort-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = ref: "-O CRAM -T ${ref}"; } {filetype = outfmtR;};
+in stdenv.mkDerivation {
   name = "samtools-sort";
   buildInputs = [ samtools ];
   buildCommand = ''
-    samtools sort -@ $NIX_BUILD_CORES ${optionalString nameSort "-n"} ${optionalString (flags != null) flags} ${input} > $out
+    samtools sort -@ $NIX_BUILD_CORES ${optionalString nameSort "-n"} ${outFmtFlags} ${optionalString (flags != null) flags} ${input} > $out
   '';
+  passthru.filetype = if nameSort then bionix.types.nameSort outfmtR else coordSort outfmtR;
 }
diff --git a/tools/samtools-view.nix b/tools/samtools-view.nix
new file mode 100644
index 0000000..e1cdac1
--- /dev/null
+++ b/tools/samtools-view.nix
@@ -0,0 +1,27 @@
+{ bionix
+, nixpkgs
+, nameSort ? false
+, flags ? null
+, outfmt ? null
+}:
+
+input:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+
+assert (matchFiletype "samtools-sort" { bam = _: true; sam = _: true; cram = _: true; } input);
+
+let
+  outfmtR = if outfmt != null then outfmt input else input.filetype;
+  fa = ref: matchFiletype "samtools-view-ref" { fa = _: ref; } ref;
+  outfmtFlags = matchFiletype "samtools-sort-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = x: "-O CRAM -T ${fa x.ref}"; } {filetype = outfmtR;};
+in stdenv.mkDerivation {
+  name = "samtools-view";
+  buildInputs = [ samtools ];
+  buildCommand = ''
+    samtools view ${outfmtFlags} ${optionalString (flags != null) flags} ${input} > $out
+  '';
+  passthru.filetype = outfmtR;
+}
diff --git a/tools/samtools.nix b/tools/samtools.nix
index 6b08c6e..89a96b0 100644
--- a/tools/samtools.nix
+++ b/tools/samtools.nix
@@ -3,6 +3,7 @@
 with bionix;
 
 {
+  view = callBionix ./samtools-view.nix;
   faidx = callBionix ./samtools-faidx.nix;
   flagstat = callBionix ./samtools-flagstat.nix;
   index = callBionix ./samtools-index.nix;
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index ecdea84..bcbb6d1 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -1,6 +1,5 @@
 { bionix
 , nixpkgs
-, ref
 , indexAttrs ? {}
 , bamIndexAttrs ? {}
 , flags ? null
@@ -10,17 +9,25 @@
 
 with nixpkgs;
 with lib;
+with bionix.types;
 
 let
   filename = path: last (splitString "/" path);
+  getref = f: matchFiletype "strelka-call" { bam = x: x.ref; } f;
   inputs = [ normal tumour ];
+  refs = map getref inputs;
+  ref = head refs;
 
-in stdenv.mkDerivation {
+in
+
+assert (length (unique refs) == 1);
+
+stdenv.mkDerivation {
   name = "strelka";
   buildInputs = [ strelka ];
   buildCommand = ''
-    ln -s ${ref.seq} ref.fa
-    ln -s ${bionix.samtools.faidx indexAttrs ref.seq} ref.fa.fai
+    ln -s ${ref} ref.fa
+    ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
     ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
     ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
 
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