diff options
| -rw-r--r-- | default.nix | 1 | ||||
| -rw-r--r-- | test-tnpair.nix | 9 | ||||
| -rw-r--r-- | tools/fastqc-app.nix | 24 | ||||
| -rw-r--r-- | tools/fastqc-check.nix | 20 | ||||
| -rw-r--r-- | tools/fastqc.nix | 7 | ||||
| -rw-r--r-- | tools/samtools-flagstat.nix | 15 | ||||
| -rw-r--r-- | tools/samtools.nix | 3 |
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; } |