diff options
| -rw-r--r-- | default.nix | 1 | ||||
| -rwxr-xr-x | lib/references.nix | 22 | ||||
| -rw-r--r-- | lib/types.nix | 3 | ||||
| -rw-r--r-- | tools/kallisto-index.nix | 22 | ||||
| -rw-r--r-- | tools/kallisto-quant.nix | 48 | ||||
| -rw-r--r-- | tools/kallisto.nix | 8 |
6 files changed, 103 insertions, 1 deletions
diff --git a/default.nix b/default.nix index 5218a99..f835fa0 100644 --- a/default.nix +++ b/default.nix @@ -15,6 +15,7 @@ let fastqc = callBionix ./tools/fastqc.nix {}; gridss = callBionix ./tools/gridss.nix {}; infercnv = callBionix ./tools/infercnv.nix {}; + kallisto = callBionix ./tools/kallisto.nix {}; mosdepth = callBionix ./tools/mosdepth.nix {}; mutect = callBionix ./tools/mutect.nix {}; platypus = callBionix ./tools/platypus.nix {}; diff --git a/lib/references.nix b/lib/references.nix index 498cfd9..bdeefa6 100755 --- a/lib/references.nix +++ b/lib/references.nix @@ -46,6 +46,28 @@ rec { ''; passthru.filetype = filetype.vcf { ref = seq; }; }; + ensembl = { + cdna = stdenvNoCC.mkDerivation rec { + name = "ensembl-grch38-cdna-${version}"; + version = "94"; + src = fetchurl { + url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz"; + sha256 = "1fc5d6p2wlwsm49wnmxmm3byjx5jvr6z9fpzrq7v7fpb086adl0h"; + }; + buildCommand = "gunzip < $src > $out"; + passthru.filetype = filetype.fa {}; + }; + ncrna = stdenvNoCC.mkDerivation rec { + name = "ensembl-grch38-ncrna-${version}"; + version = "94"; + src = fetchurl { + url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz"; + sha256 = "1cpasykwriila52nqgvw6d3mjyh6d9qi613hvhn4h1dxkqzgnjff"; + }; + buildCommand = "gunzip < $src > $out"; + passthru.filetype = filetype.fa {}; + }; + }; }; grcm38 = grcm38-p6; diff --git a/lib/types.nix b/lib/types.nix index 4dbc6ff..ef9b1b7 100644 --- a/lib/types.nix +++ b/lib/types.nix @@ -21,7 +21,8 @@ let in rec { - matchFiletype = sym: y: x: if x ? filetype then match x.filetype (defError (idft sym) y filetype) else abort "unknown filetype for ${sym}"; + matchFiletype = sym: y: x: if x ? filetype then matchFiletype' sym y x.filetype else abort "unknown filetype for ${sym}"; + matchFiletype' = sym: y: x: match x (defError (idft sym) y filetype); filetype = make-type "filetype" { fa = {}; fq = {}; diff --git a/tools/kallisto-index.nix b/tools/kallisto-index.nix new file mode 100644 index 0000000..33dfb80 --- /dev/null +++ b/tools/kallisto-index.nix @@ -0,0 +1,22 @@ +{bionix +, nixpkgs +, kmerSize ? 31 +, unique ? false}: + +with nixpkgs; +with lib; +with bionix.types; + +assert (kmerSize > 1); + +input: + +assert (matchFiletype input { fa = _: true; } input); + +stdenv.mkDerivation { + name = "kallisto-index"; + buildInputs = [ kallisto ]; + buildCommand = '' + kallisto index -k ${toString kmerSize} ${optionalString unique "--make-unique"} -i $out ${input} + ''; +} diff --git a/tools/kallisto-quant.nix b/tools/kallisto-quant.nix new file mode 100644 index 0000000..c410721 --- /dev/null +++ b/tools/kallisto-quant.nix @@ -0,0 +1,48 @@ +{bionix +, nixpkgs +, indexFlags ? {} +, bias ? false +, bootstrapSamples ? 0 +, seed ? 42 +, plaintext ? false +, fusion ? false +, single ? false +, frStranded ? false +, rfStranded ? false +, fragmentLength ? null +, fragmentSD ? null +, ref}: + +with nixpkgs; +with lib; + +assert (!single || (fragmentLength != null && fragmentSD != null)); + +inputs: + +let + inherit (bionix.types) matchFiletype'; + isFastQ = matchFiletype' "kallisto-quant" {fq = _: true; gz = isFastQ; }; +in + +assert (all (x: isFastQ (x.filetype)) inputs); + +stdenv.mkDerivation { + name = "kallisto-quant"; + buildInputs = [ kallisto ]; + buildCommand = '' + mkdir $out + kallisto quant \ + -i ${bionix.kallisto.index indexFlags ref} \ + -o $out \ + ${optionalString bias "--bias"} \ + ${optionalString (bootstrapSamples > 0) "-b ${toString bootstrapSamples} --seed=${toString seed}"} \ + ${optionalString plaintext "--plaintext"} \ + ${optionalString fusion "--fusion"} \ + ${optionalString single "--single -l ${toString fragmentLength} -s ${toString fragmentSD}"} \ + ${optionalString frStranded "--fr-stranded"} \ + ${optionalString rfStranded "--rf-stranded"} \ + -t $NIX_BUILD_CORES \ + ${concatStringsSep " " inputs} + ''; +} diff --git a/tools/kallisto.nix b/tools/kallisto.nix new file mode 100644 index 0000000..f13f493 --- /dev/null +++ b/tools/kallisto.nix @@ -0,0 +1,8 @@ +{bionix, nixpkgs}: + +with bionix; + +{ + index = callBionix ./kallisto-index.nix; + quant = callBionix ./kallisto-quant.nix; +} |