Add flagstat and fastqc

7 files changed, 78 insertions, 1 deletions

diff --git a/default.nix b/default.nix
index a9fb72b..a5c9f3f 100644
--- a/default.nix
+++ b/default.nix
@@ -5,6 +5,7 @@ let
     let callBionix = file: import file { bionix = self; nixpkgs = nixpkgs; };
     in with self; {
       bwa = callBionix ./tools/bwa.nix;
+      fastqc = callBionix ./tools/fastqc.nix;
       mosdepth = callBionix ./tools/mosdepth.nix;
       platypus = callBionix ./tools/platypus.nix;
       ref = callBionix ./references.nix;
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 31570ee..ef2af1b 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -6,6 +6,8 @@ let
   ref = ./example/ref.fa;
   alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
   sort = samtools.sort { };
+  flagstat = samtools.flagstat {};
+  check = fastqc.check {};
   callVariants = strelka.call { inherit ref; };
 
   tnpair = { tumour = {name = "mysample1"; files = {input1 = ./example/sample1-1.fq; input2 = ./example/sample1-2.fq;};};
@@ -26,6 +28,13 @@ let
       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 ${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
+      ln -s ${check tnpair.tumour.files.input1} $out/fastqc/${tnpair.tumour.name}.1
+      ln -s ${check tnpair.tumour.files.input2} $out/fastqc/${tnpair.tumour.name}.2
+      ln -s ${check tnpair.normal.files.input1} $out/fastqc/${tnpair.normal.name}.1
+      ln -s ${check tnpair.normal.files.input2} $out/fastqc/${tnpair.normal.name}.2
     '';
   };
 
diff --git a/tools/fastqc-app.nix b/tools/fastqc-app.nix
new file mode 100644
index 0000000..40fd7ec
--- /dev/null
+++ b/tools/fastqc-app.nix
@@ -0,0 +1,24 @@
+{ stdenv, unzip, perl, fetchurl, jre }:
+
+stdenv.mkDerivation rec {
+  name = "fastqc-${version}";
+  version = "0.11.7";
+
+  src = fetchurl {
+    url = "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip";
+    sha256 = "04hifbfrh60s5kzqr7n46bcviaiymr1rx67b88s3cpxydf3m1ksr";
+  };
+
+  buildInputs = [ unzip perl ];
+
+  phases = [ "unpackPhase" "installPhase" "fixupPhase" ];
+
+  installPhase = ''
+    mkdir -p $out/libexec/fastqc
+    cp -r . $out/libexec/fastqc
+    mkdir $out/bin
+    ln -s $out/libexec/fastqc/fastqc $out/bin
+    substituteInPlace $out/bin/fastqc --replace "my \$java_bin = 'java'" "my \$java_bin = '${jre}/bin/java'"
+    chmod 755 $out/libexec/fastqc/fastqc
+  '';
+}
diff --git a/tools/fastqc-check.nix b/tools/fastqc-check.nix
new file mode 100644
index 0000000..e13ce2a
--- /dev/null
+++ b/tools/fastqc-check.nix
@@ -0,0 +1,20 @@
+{ stdenv
+, lib
+, fastqc
+, flags ? null}:
+
+with lib;
+
+input:
+
+stdenv.mkDerivation {
+  name = "fastqc-check";
+  buildInputs = [ fastqc ];
+  buildCommand = ''
+    mkdir $out
+    fastqc \
+      -o $out \
+      ${optionalString (flags != null) flags} \
+      ${input}
+  '';
+}
diff --git a/tools/fastqc.nix b/tools/fastqc.nix
new file mode 100644
index 0000000..2034c91
--- /dev/null
+++ b/tools/fastqc.nix
@@ -0,0 +1,7 @@
+{ bionix, nixpkgs }:
+
+with nixpkgs;
+
+{
+  check = attrs: callPackage ./fastqc-check.nix attrs;
+}
diff --git a/tools/samtools-flagstat.nix b/tools/samtools-flagstat.nix
new file mode 100644
index 0000000..790eeb4
--- /dev/null
+++ b/tools/samtools-flagstat.nix
@@ -0,0 +1,15 @@
+{ stdenv
+, callPackage
+, lib
+, samtools
+}:
+
+input:
+
+with lib;
+
+stdenv.mkDerivation {
+  name = "samtools-index";
+  buildInputs = [ samtools ];
+  buildCommand = "samtools flagstat -@ $NIX_BUILD_CORES ${input} > $out";
+}
diff --git a/tools/samtools.nix b/tools/samtools.nix
index 6fdbef5..77e3815 100644
--- a/tools/samtools.nix
+++ b/tools/samtools.nix
@@ -3,7 +3,8 @@
 with nixpkgs;
 
 {
+  faidx = attrs: callPackage ./samtools-faidx.nix attrs;
+  flagstat = attrs: callPackage ./samtools-flagstat.nix attrs;
   index = attrs: callPackage ./samtools-index.nix attrs;
   sort = attrs: callPackage ./samtools-sort.nix attrs;
-  faidx = attrs: callPackage ./samtools-faidx.nix attrs;
 }