diff options
| -rw-r--r-- | default.nix | 3 | ||||
| -rw-r--r-- | test-tnpair.nix | 2 | ||||
| -rw-r--r-- | tools/facets-app.nix | 42 | ||||
| -rw-r--r-- | tools/facets-call.nix | 24 | ||||
| -rw-r--r-- | tools/facets.nix | 8 |
5 files changed, 78 insertions, 1 deletions
diff --git a/default.nix b/default.nix index 3ed2b50..0c2f9ad 100644 --- a/default.nix +++ b/default.nix @@ -18,6 +18,7 @@ let cnvkit = callBionix ./tools/cnvkit.nix {}; compression = callBionix ./tools/compression.nix {}; crumble = callBionix ./tools/crumble.nix {}; + facets = callBionix ./tools/facets.nix {}; fastqc = callBionix ./tools/fastqc.nix {}; gridss = callBionix ./tools/gridss.nix {}; infercnv = callBionix ./tools/infercnv.nix {}; @@ -25,10 +26,10 @@ let mosdepth = callBionix ./tools/mosdepth.nix {}; mutect = callBionix ./tools/mutect.nix {}; platypus = callBionix ./tools/platypus.nix {}; + ref = callBionix ./lib/references.nix {}; samtools = callBionix ./tools/samtools.nix {}; snpeff = callBionix ./tools/snpeff.nix {}; strelka = callBionix ./tools/strelka.nix {}; - ref = callBionix ./lib/references.nix {}; qsub = attrs: bionix.extend (self: super: with self; rec { qsubDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; tmpDir = "/tmp"; sleepTime = 60; } // attrs; diff --git a/test-tnpair.nix b/test-tnpair.nix index 0851a74..c531a83 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -35,11 +35,13 @@ let processPair = { tumour, normal }: rec { alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG x.name x.files)))) { inherit normal tumour; }; variants = callVariants alignments; + platypusVars = platypus.call {} (builtins.attrValues alignments); }; tnpairResult = processPair tnpair; testNaming = linkDrv [ + (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets") (ln tnpairResult.variants "strelka") (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam") (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss") diff --git a/tools/facets-app.nix b/tools/facets-app.nix new file mode 100644 index 0000000..8c4a7b2 --- /dev/null +++ b/tools/facets-app.nix @@ -0,0 +1,42 @@ +{buildRPackage +,fetchFromGitHub +,R +,htslib +,zlib}: + +let + pctGCdata = buildRPackage rec { + name = "pctGCdata-${version}"; + version = "0.2.0"; + requireX = false; + src = fetchFromGitHub { + owner = "mskcc"; + repo = "pctGCdata"; + rev = "v${version}"; + sha256 = "1qq0fmm3zwz6rv0ka82850ww0qj50621gln9i0gfs8k3wyqil4l8"; + }; + buildInputs = [ R ]; + }; + +in buildRPackage rec{ + name = "facets-${version}"; + version = "0.5.6"; + requireX = false; + src = fetchFromGitHub { + owner = "mskcc"; + repo = "facets"; + rev = "v${version}"; + sha256 = "0yqr23446y2h8xgbgj0r6sl4i778111drgsi06a2cqy530xcmbxs"; + }; + buildInputs = [ R htslib zlib ]; + propagatedBuildInputs = [ pctGCdata ]; + postBuild = '' + cd inst/extcode + g++ --std=c++11 snp-pileup.cpp -lhts -o snp-pileup + cd ../../ + ''; + postInstall = '' + mkdir -p $out/bin + cp inst/extcode/snp-pileup $out/bin + ''; +} diff --git a/tools/facets-call.nix b/tools/facets-call.nix new file mode 100644 index 0000000..021cacc --- /dev/null +++ b/tools/facets-call.nix @@ -0,0 +1,24 @@ +{bionix}: + +{vcf, bams}: + +with bionix; +with types; +with lib; + +assert (matchFiletype "facets-call-vcf" { vcf = _: true; } vcf); +assert (all (matchFiletype "facets-call-bam" { bam = _: true; }) bams); +assert (all (matchFileSorting "facets-call-bam" { coord = _: true; }) bams); + +stage { + name = "facets"; + buildInputs = [ facets.app ]; + buildCommand = '' + # Facets requires lexical sorting on the VCF files + grep '^#' ${vcf} > input.vcf + grep -v '^#' ${vcf} | LC_ALL=C sort -t $'\t' -k1,1 -k2,2n >> input.vcf || true + + # Now actually run facets + snp-pileup input.vcf $out ${concatStringsSep " " bams} + ''; +} diff --git a/tools/facets.nix b/tools/facets.nix new file mode 100644 index 0000000..ed10ffa --- /dev/null +++ b/tools/facets.nix @@ -0,0 +1,8 @@ +{bionix}: + +with bionix; + +{ + app = lib.callPackageWith (pkgs // pkgs.rPackages) ./facets-app.nix {}; + callCNV = callBionix ./facets-call.nix; +} |