diff options
| -rw-r--r-- | default.nix | 1 | ||||
| -rw-r--r-- | test-tnpair.nix | 11 | ||||
| -rw-r--r-- | tools/bowtie-align.nix | 36 | ||||
| -rw-r--r-- | tools/bowtie-index.nix | 22 | ||||
| -rw-r--r-- | tools/bowtie.nix | 8 |
5 files changed, 74 insertions, 4 deletions
diff --git a/default.nix b/default.nix index 50b85a3..d607aa2 100644 --- a/default.nix +++ b/default.nix @@ -12,6 +12,7 @@ let types = callBionix ./lib/types.nix {}; bwa = callBionix ./tools/bwa.nix {}; + bowtie = callBionix ./tools/bowtie.nix {}; compression = callBionix ./tools/compression.nix {}; crumble = callBionix ./tools/crumble.nix {}; fastqc = callBionix ./tools/fastqc.nix {}; diff --git a/test-tnpair.nix b/test-tnpair.nix index a6ea163..b01d61e 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -21,7 +21,9 @@ let fetchfq = attrs: types.tagFiletype (types.filetype.fq {}) (fetchlocal attrs); fetchfa = attrs: types.tagFiletype (types.filetype.fa {}) (fetchlocal attrs); - alignWithRG = rg: bwa.align { ref = fetchfa ./example/ref.fa; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";}; + ref = fetchfa ./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 {}; @@ -35,7 +37,7 @@ let }; normal = {name = "mysample2"; files = { input1 = fetchfq ./example/sample2-1.fq; - input2 = fetchfq ./example/sample2-1.fq; + input2 = fetchfq ./example/sample2-2.fq; }; }; }; @@ -53,8 +55,9 @@ let mkdir $out ln -s ${tnpairResult.variants} $out/strelka mkdir $out/alignments - ln -s ${gridss.callVariants {} (with tnpairResult.alignments; [tumour])} $out/gridss - ln -s ${gridss.call (with tnpairResult.alignments; [tumour])} $out/gridss2 + ln -s ${bowtie.align {inherit ref;} tnpair.normal.files} $out/alignments/bowtie-normal.bam + ln -s ${gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])} $out/gridss + ln -s ${gridss.call (with tnpairResult.alignments; [normal tumour])} $out/gridss2 ln -s ${samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]} $out/alignments/merged.bam ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)} $out/alignments/${tnpair.tumour.name}.cram ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)} $out/alignments/${tnpair.normal.name}.cram diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix new file mode 100644 index 0000000..456747a --- /dev/null +++ b/tools/bowtie-align.nix @@ -0,0 +1,36 @@ +{ bionix +, nixpkgs +, ref +, bamOutput ? true +, flags ? null +, indexAttrs ? {} +}: + +{ input1 +, input2 ? null +}: + +with nixpkgs; +with lib; +with bionix.types; +with bionix.compression; + +let + fa = f: matchFiletype "bowtie2-ref" { fa = _: f; } f; + fq = f: matchFiletype "bowtie2-input" { fq = _: f; gz = matchFiletype' "bowtie2-input" { fq = _: f; }; } f; + +in stdenv.mkDerivation { + name = "bowtie2-align"; + buildInputs = [ bowtie2 bc ] ++ optional bamOutput samtools; + buildCommand = '' + cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc) + if [[ $cores -lt 1 ]] ; then + cores=1 + fi + bowtie2 -x ${bionix.bowtie.index indexAttrs ref}/ref ${optionalString (flags != null) flags} --threads $cores \ + ${if input2 != null then "-1 " + fq input1 + " -2 " + fq input2 else "-U " + fq input1} \ + ${optionalString bamOutput "| samtools view -b"} \ + > $out + ''; + passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};}; +} diff --git a/tools/bowtie-index.nix b/tools/bowtie-index.nix new file mode 100644 index 0000000..98e529f --- /dev/null +++ b/tools/bowtie-index.nix @@ -0,0 +1,22 @@ +{ bionix +, nixpkgs +, flags ? null +, seed ? 42 +}: + +ref: + +with nixpkgs; +with lib; +with bionix.types; + +assert (matchFiletype "bowtie-index" { fa = _: true; } ref); + +stdenv.mkDerivation { + name = "bowtie-index"; + buildInputs = [ bowtie2 ]; + buildCommand = '' + mkdir $out + bowtie2-build --seed ${toString seed} --threads $NIX_BUILD_CORES ${optionalString (flags != null) flags} ${ref} $out/ref + ''; +} diff --git a/tools/bowtie.nix b/tools/bowtie.nix new file mode 100644 index 0000000..a9fa2e8 --- /dev/null +++ b/tools/bowtie.nix @@ -0,0 +1,8 @@ +{ bionix, nixpkgs }: + +with bionix; + +{ + align = callBionix ./bowtie-align.nix; + index = callBionix ./bowtie-index.nix; +} |