diff options
| -rw-r--r-- | default.nix | 14 | ||||
| -rw-r--r-- | references.nix | 18 | ||||
| -rw-r--r-- | test-tnpair.nix | 14 | ||||
| -rw-r--r-- | tools/bwa-index.nix | 1 | ||||
| -rw-r--r-- | tools/bwa-mem.nix | 40 | ||||
| -rw-r--r-- | tools/bwa.nix | 36 | ||||
| -rw-r--r-- | tools/mosdepth-depth.nix | 14 | ||||
| -rw-r--r-- | tools/mosdepth-plot.nix | 15 | ||||
| -rw-r--r-- | tools/mosdepth.nix | 8 | ||||
| -rw-r--r-- | tools/platypus-callVariants.nix | 33 | ||||
| -rw-r--r-- | tools/platypus.nix | 34 | ||||
| -rw-r--r-- | tools/samtools.nix | 9 | ||||
| -rw-r--r-- | tools/strelka-call.nix | 40 | ||||
| -rw-r--r-- | tools/strelka.nix | 41 |
14 files changed, 211 insertions, 106 deletions
diff --git a/default.nix b/default.nix new file mode 100644 index 0000000..a9fb72b --- /dev/null +++ b/default.nix @@ -0,0 +1,14 @@ +{nixpkgs ? import <nixpkgs> {}}: + +let + bionix = nixpkgs.lib.makeExtensible (self: + let callBionix = file: import file { bionix = self; nixpkgs = nixpkgs; }; + in with self; { + bwa = callBionix ./tools/bwa.nix; + mosdepth = callBionix ./tools/mosdepth.nix; + platypus = callBionix ./tools/platypus.nix; + ref = callBionix ./references.nix; + samtools = callBionix ./tools/samtools.nix; + strelka = callBionix ./tools/strelka.nix; + }); +in bionix diff --git a/references.nix b/references.nix new file mode 100644 index 0000000..e7f1c7a --- /dev/null +++ b/references.nix @@ -0,0 +1,18 @@ +{ bionix, nixpkgs }: + +with nixpkgs; + +rec { + grch38 = grch38-p12; + grch38-p12 = { + seq = stdenv.mkDerivation rec { + name = "seq-grch38.${version}"; + version = "p12"; + src = fetchurl { + url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/GRCh38.p12.genome.fa.gz"; + sha256 = "0ji2ggpmgnbpwbhq8mirj6h3lyy02nl2rnz7n892iq5cqpsblh4z"; + }; + buildCommand = "gunzip < $src > $out"; + }; + }; +} diff --git a/test-tnpair.nix b/test-tnpair.nix index b3a41cb..31570ee 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -1,23 +1,21 @@ -{pkgs ? import <nixpkgs> {}}: - -with pkgs; +with (import <nixpkgs> {}); +with (import <bionix> {}); with lib; let ref = ./example/ref.fa; - alignWithRG = rg: callPackage ./tools/bwa.nix { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";}; - sort = callPackage ./tools/samtools-sort.nix { }; - callVariants = callPackage ./tools/strelka.nix { inherit ref; }; + alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";}; + sort = samtools.sort { }; + callVariants = strelka.call { inherit ref; }; 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;};};}; + normal = {name = "mysample2"; files = {input1 = ./example/sample2-1.fq; input2 = ./example/sample2-1.fq;};};}; processPair = { tumour, normal }: rec { alignments = mapAttrs (_: x: sort (alignWithRG x.name x.files)) { inherit normal tumour; }; variants = callVariants alignments; }; - #results = map processPair tnpairs; tnpairResult = processPair tnpair; testNaming = stdenv.mkDerivation { diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix index 8ca0eec..b5e3779 100644 --- a/tools/bwa-index.nix +++ b/tools/bwa-index.nix @@ -15,5 +15,6 @@ stdenv.mkDerivation { bwa index ref.fa mkdir $out mv ref.fa.* $out + grep '^>[^ \t]*_alt$' ref.fa | tr -d '^>' > $out/idxbase.alt || true ''; } diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix new file mode 100644 index 0000000..5a2772e --- /dev/null +++ b/tools/bwa-mem.nix @@ -0,0 +1,40 @@ +{ stdenv +, callPackage +, lib +, bc +, bwa +, samtools ? null +, ref +, bamOutput ? true +, flags ? null +}: + +{ input1 +, input2 ? null +}: + +assert bamOutput -> samtools != null; + +with lib; + +let index = callPackage ./bwa-index.nix { inherit bwa stdenv lib; } ref; + +in stdenv.mkDerivation { + name = "bwa-mem"; + buildInputs = [ bwa bc ] ++ optional bamOutput samtools; + buildCommand = '' + ln -s ${ref} ref.fa + for f in ${index}/* ; do + ln -s $f + done + cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc) + if [[ $cores -lt 1 ]] ; then + >&2 echo "not enough build cores" + exit 1 + fi + bwa mem ${optionalString (flags != null) flags} -t $cores ref.fa ${input1} \ + ${optionalString (input2 != null) input2} \ + ${optionalString bamOutput "| samtools view -b"} \ + > $out + ''; +} diff --git a/tools/bwa.nix b/tools/bwa.nix index 20a308f..df61cba 100644 --- a/tools/bwa.nix +++ b/tools/bwa.nix @@ -1,34 +1,8 @@ -{ stdenv -, callPackage -, lib -, bwa -, samtools ? null -, ref -, bamOutput ? true -, flags ? null -}: +{ bionix, nixpkgs }: -{ input1 -, input2 ? null -}: +with nixpkgs; -assert bamOutput -> samtools != null; - -with lib; - -let index = callPackage ./bwa-index.nix { inherit bwa stdenv lib; } ref; - -in stdenv.mkDerivation { - name = "bwa-mem"; - buildInputs = [ bwa ] ++ optional bamOutput samtools; - buildCommand = '' - ln -s ${ref} ref.fa - for f in ${index}/* ; do - ln -s $f - done - bwa mem ${optionalString (flags != null) flags} -t $NIX_BUILD_CORES ref.fa ${input1} \ - ${optionalString (input2 != null) input2} \ - ${optionalString bamOutput "| samtools view -b"} \ - > $out - ''; +{ + align = attrs: callPackage ./bwa-mem.nix attrs; + index = attrs: callPackage ./bwa-index.nix attrs; } diff --git a/tools/mosdepth-depth.nix b/tools/mosdepth-depth.nix new file mode 100644 index 0000000..3340872 --- /dev/null +++ b/tools/mosdepth-depth.nix @@ -0,0 +1,14 @@ +{ stdenv +, mosdepth +, flags ? null}: + +input: + +stdenv.mkDerivation { + name = "mosdepth-depth"; + buildInputs = [ mosdepth ]; + buildCommand = '' + mkdir $out + mosdepth -t $NIX_BUILD_CORES ${optionalString (flags != null) flags} $out/out ${input} + ''; +} diff --git a/tools/mosdepth-plot.nix b/tools/mosdepth-plot.nix new file mode 100644 index 0000000..464e495 --- /dev/null +++ b/tools/mosdepth-plot.nix @@ -0,0 +1,15 @@ +{ stdenv +, mosdepth +, python +, flags ? null}: + +input: + +stdenv.mkDerivation { + name = "mosdepth-depth"; + buildInputs = [ python ]; + buildCommand = '' + python ${mosdepth.src}/scripts/plot-dist.py ${input}/*global.dist.txt + mv dist.html $out + ''; +} diff --git a/tools/mosdepth.nix b/tools/mosdepth.nix new file mode 100644 index 0000000..447e530 --- /dev/null +++ b/tools/mosdepth.nix @@ -0,0 +1,8 @@ +{ bionix, nixpkgs }: + +with nixpkgs; + +{ + depth = attrs: callPackage ./mosdepth-depth.nix attrs; + plot = attrs: callPackage ./mosdepth-plot.nix attrs; +} diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix new file mode 100644 index 0000000..3e150d2 --- /dev/null +++ b/tools/platypus-callVariants.nix @@ -0,0 +1,33 @@ +{ stdenv +, callPackage +, lib +, platypus +, ref +, index ? callPackage ./samtools-faidx.nix {} +, bamIndex ? callPackage ./samtools-index.nix {} +, flags ? null +}: + +inputs: + +with lib; + +let filename = path: last (splitString "/" path); + +in stdenv.mkDerivation { + name = "platypus"; + buildInputs = [ platypus ]; + buildCommand = '' + ln -s ${ref} ref.fa + ln -s ${index ref} ref.fa.fai + ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs} + ${concatMapStringsSep "\n" (p: "ln -s ${bamIndex p} ${filename p}.bai") inputs} + ls -l + platypus callVariants \ + --nCPU=$NIX_BUILD_CORES \ + --refFile=ref.fa \ + ${optionalString (flags != null) flags} \ + -o $out \ + --bamFiles=${concatMapStringsSep "," (p: "${filename p}.bam") inputs} + ''; +} diff --git a/tools/platypus.nix b/tools/platypus.nix index 3e150d2..88d88d7 100644 --- a/tools/platypus.nix +++ b/tools/platypus.nix @@ -1,33 +1,7 @@ -{ stdenv -, callPackage -, lib -, platypus -, ref -, index ? callPackage ./samtools-faidx.nix {} -, bamIndex ? callPackage ./samtools-index.nix {} -, flags ? null -}: +{ bionix, nixpkgs }: -inputs: +with nixpkgs; -with lib; - -let filename = path: last (splitString "/" path); - -in stdenv.mkDerivation { - name = "platypus"; - buildInputs = [ platypus ]; - buildCommand = '' - ln -s ${ref} ref.fa - ln -s ${index ref} ref.fa.fai - ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs} - ${concatMapStringsSep "\n" (p: "ln -s ${bamIndex p} ${filename p}.bai") inputs} - ls -l - platypus callVariants \ - --nCPU=$NIX_BUILD_CORES \ - --refFile=ref.fa \ - ${optionalString (flags != null) flags} \ - -o $out \ - --bamFiles=${concatMapStringsSep "," (p: "${filename p}.bam") inputs} - ''; +{ + call = attrs: callPackage ./platypus-callVariants.nix attrs; } diff --git a/tools/samtools.nix b/tools/samtools.nix new file mode 100644 index 0000000..6fdbef5 --- /dev/null +++ b/tools/samtools.nix @@ -0,0 +1,9 @@ +{ bionix, nixpkgs }: + +with nixpkgs; + +{ + index = attrs: callPackage ./samtools-index.nix attrs; + sort = attrs: callPackage ./samtools-sort.nix attrs; + faidx = attrs: callPackage ./samtools-faidx.nix attrs; +} diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix new file mode 100644 index 0000000..ec7a764 --- /dev/null +++ b/tools/strelka-call.nix @@ -0,0 +1,40 @@ +{ stdenv +, callPackage +, lib +, strelka +, ref +, index ? callPackage ./samtools-faidx.nix {} +, bamIndex ? callPackage ./samtools-index.nix {} +, flags ? null +}: + +{normal, tumour}: + +with lib; + +let + filename = path: last (splitString "/" path); + inputs = [ normal tumour ]; + +in stdenv.mkDerivation { + name = "strelka"; + buildInputs = [ strelka ]; + buildCommand = '' + ln -s ${ref} ref.fa + ln -s ${index ref} ref.fa.fai + ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs} + ${concatMapStringsSep "\n" (p: "ln -s ${bamIndex p} ${filename p}.bai") inputs} + + configureStrelkaSomaticWorkflow.py \ + --normalBam ${filename normal}.bam \ + --tumourBam ${filename tumour}.bam \ + --ref ref.fa \ + --runDir $TMPDIR + + ./runWorkflow.py \ + -m local \ + -j $NIX_BUILD_CORES + + cp -r results $out + ''; +} diff --git a/tools/strelka.nix b/tools/strelka.nix index ec7a764..a115740 100644 --- a/tools/strelka.nix +++ b/tools/strelka.nix @@ -1,40 +1,7 @@ -{ stdenv -, callPackage -, lib -, strelka -, ref -, index ? callPackage ./samtools-faidx.nix {} -, bamIndex ? callPackage ./samtools-index.nix {} -, flags ? null -}: +{ bionix, nixpkgs }: -{normal, tumour}: +with nixpkgs; -with lib; - -let - filename = path: last (splitString "/" path); - inputs = [ normal tumour ]; - -in stdenv.mkDerivation { - name = "strelka"; - buildInputs = [ strelka ]; - buildCommand = '' - ln -s ${ref} ref.fa - ln -s ${index ref} ref.fa.fai - ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs} - ${concatMapStringsSep "\n" (p: "ln -s ${bamIndex p} ${filename p}.bai") inputs} - - configureStrelkaSomaticWorkflow.py \ - --normalBam ${filename normal}.bam \ - --tumourBam ${filename tumour}.bam \ - --ref ref.fa \ - --runDir $TMPDIR - - ./runWorkflow.py \ - -m local \ - -j $NIX_BUILD_CORES - - cp -r results $out - ''; +{ + call = attrs: callPackage ./strelka-call.nix attrs; } |