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with import <bionix> { };
with lib;
let
fetchlocal = path: pkgs.stdenv.mkDerivation {
name = baseNameOf path;
buildCommand = "ln -s ${path} $out";
};
fetchfq = attrs: types.tagFiletype (types.filetype.fq { }) (fetchlocal attrs);
fetchfa = attrs: types.tagFiletype (types.filetype.fa { }) (fetchlocal attrs);
ref = fetchfa ./examples/ref.fa;
alignWithRG = aligner: rg: x: nameSort (aligner { inherit ref; RG = { ID = rg; SM = rg; }; } x);
sort = sambamba.sort { };
nameSort = sambamba.sort { nameSort = true; };
flagstat = samtools.flagstat { };
check-fastqc = fastqc.check { };
check-fastp = fastp.check { };
callVariants = strelka.callSomatic { };
markdup = samtools.markdup { };
fixmate = samtools.fixmate { };
tnpair = {
tumour = {
name = "mysample1";
files = {
input1 = fetchfq ./examples/sample1-1.fq;
input2 = fetchfq ./examples/sample1-2.fq;
};
};
normal = {
name = "mysample2";
files = {
input1 = fetchfq ./examples/sample2-1.fq;
input2 = fetchfq ./examples/sample2-2.fq;
};
};
};
processPair = { tumour, normal }: rec {
alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG bwa.align x.name x.files)))) { inherit normal tumour; };
bowtie-alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG bowtie.align x.name x.files)))) { inherit normal tumour; };
bwa2-alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG bwa.mem2 x.name x.files)))) { inherit normal tumour; };
variants = callVariants alignments;
octopusSomatic = octopus.callSomatic { } { inherit (alignments) normal; tumours = [ alignments.tumour ]; };
glvariants = strelka.call { } (builtins.attrValues alignments);
platypusVars = platypus.call { } (builtins.attrValues alignments);
octopusVars = octopus.call { } (builtins.attrValues alignments);
shards = map (x: nameSort (bwa.align { inherit ref; } x)) (shard.fastQPair 2 normal.files);
};
tnpairResult = processPair tnpair;
cnvkitResults = rec {
cnvs = cnvkit.callCNV { } (with tnpairResult.alignments; { normals = [ normal ]; tumours = [ tumour ]; });
plot = cnvkit.scatterPlot { } cnvs.out1;
};
alignments = {
"bowtie-normal.bam" = bowtie.align { inherit ref; } tnpair.normal.files;
"subread.bam" = subread.align { inherit ref; } tnpair.normal.files;
"last.maf" = lastal.align { inherit ref; } tnpair.normal.files;
"whisper.bam" = whisper.align { inherit ref; } tnpair.normal.files;
"bwa-mem.bam" = bwa.mem { inherit ref; } tnpair.normal.files;
"bwa-mem2.bam" = bwa.mem2 { inherit ref; } tnpair.normal.files;
"minimap2-normal.bam" = minimap2.align { inherit ref; preset = "sr"; } tnpair.normal.files;
"snap-normal.bam" = snap.align { inherit ref; } tnpair.normal.files;
"${tnpair.tumour.name}.flagstat" = flagstat tnpairResult.alignments.tumour;
"hisat2-normal.bam" = hisat2.align { inherit ref; } tnpair.normal.files;
};
testNaming = linkOutputs {
crai = samtools.index { } (samtools.view { outfmt = types.toCram; } tnpairResult.alignments.tumour);
kallisto = kallisto.quant { inherit ref; } (attrValues tnpair.tumour.files);
facets = facets.callCNV { vcf = tnpairResult.platypusVars; } (with tnpairResult.alignments; [ normal tumour ]);
cnvkit = cnvkitResults.cnvs;
"cnvkit.pdf" = cnvkitResults.plot;
"octopus.vcf" = tnpairResult.octopusVars;
"octopus-somatic.vcf" = tnpairResult.octopusSomatic;
strelka-indels = tnpairResult.variants.indels;
"strelka.snvs.vcf" = tnpairResult.variants.snvs;
"strelka.gl.vcf" = tnpairResult.glvariants;
delly = delly.call { } (with tnpairResult.alignments; [ normal tumour ]);
manta = manta.call { } (with tnpairResult.alignments; { normals = [ normal tumour ]; });
mantaTN = manta.call { } (with tnpairResult.alignments; { normals = [ normal ]; inherit tumour; });
mantaT = manta.call { } (with tnpairResult.alignments; { inherit tumour; });
gridss = gridss.callVariants { } (with tnpairResult.alignments; [ normal tumour ]);
gridss2 = gridss.call (with tnpairResult.alignments; [ normal tumour ]);
gridss3 = gridss.callAndAssemble (with tnpairResult.alignments; [ normal tumour ]);
gridssSomatic = gridss.filterSomatic { normalName = "mysample2"; } (gridss.call (with tnpairResult.alignments; [ normal tumour ]));
"merged-shards.bam" = samtools.merge { } tnpairResult.shards;
"merged.bam" = samtools.merge { } [ tnpairResult.alignments.tumour tnpairResult.alignments.normal ];
"merged-namesorted.bam" = samtools.merge { } [ (nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal) ];
"${tnpair.tumour.name}.cram" = samtools.view { outfmt = types.toCram; } tnpairResult.alignments.tumour;
"${tnpair.tumour.name}.fastqc.1" = check-fastqc tnpair.tumour.files.input1;
"${tnpair.tumour.name}.fastp" = check-fastp tnpair.tumour.files;
snver = snver.call { ploidy = 1; } tnpairResult.alignments;
mosdepth = mosdepth.plot { } { inputs = mapAttrsToList (_: mosdepth.depth { }) tnpairResult.alignments; names = [ "seq1" "seq2" ]; };
xenomapper = xenomapper.allocate { } { primary = nameSort tnpairResult.alignments.tumour; secondary = nameSort tnpairResult.alignments.tumour; };
quip = with quip; unquip {} (quip {} tnpairResult.alignments.tumour);
genmap = genmap.calcmap { } ref;
inherit alignments;
};
in
testNaming
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