Add flagstat and fastqc

5 files changed, 68 insertions, 1 deletions

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;
 }