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with import <bionix> {};
with lib;
let
fetchlocal = path: pkgs.stdenv.mkDerivation {
name = baseNameOf path;
buildCommand = "ln -s ${path} $out";
};
fetchfq = attrs: types.tagFiletype (types.filetype.fq {}) (fetchlocal attrs);
fetchfa = attrs: types.tagFiletype (types.filetype.fa {}) (fetchlocal attrs);
ref = fetchfa ./examples/ref.fa;
alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
sort = samtools.sort {};
nameSort = samtools.sort {nameSort = true;};
flagstat = samtools.flagstat {};
check-fastqc = fastqc.check {};
check-fastp = fastp.check {};
callVariants = strelka.callSomatic {};
markdup = samtools.markdup {};
fixmate = samtools.fixmate {};
tnpair = {
tumour = {name = "mysample1"; files = {
input1 = fetchfq ./examples/sample1-1.fq;
input2 = fetchfq ./examples/sample1-2.fq;
};
};
normal = {name = "mysample2"; files = {
input1 = fetchfq ./examples/sample2-1.fq;
input2 = fetchfq ./examples/sample2-2.fq;
};
};
};
processPair = { tumour, normal }: rec {
alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG x.name x.files)))) { inherit normal tumour; };
variants = callVariants alignments;
octopusSomatic = octopus.callSomatic {} {inherit (alignments) normal; tumours = [ alignments.tumour ];};
glvariants = strelka.call {} (builtins.attrValues alignments);
platypusVars = platypus.call {} (builtins.attrValues alignments);
octopusVars = octopus.call {} (builtins.attrValues alignments);
shards = map (bwa.align {inherit ref;}) (shard.fastQPair 2 normal.files);
};
tnpairResult = processPair tnpair;
cnvkitResults = rec {
cnvs = cnvkit.callCNV {} (with tnpairResult.alignments; { normals = [ normal ]; tumours = [ tumour ];});
plot = cnvkit.scatterPlot {} cnvs.out1;
};
alignments = {
"bowtie-normal.bam" = bowtie.align {inherit ref;} tnpair.normal.files;
"last.maf" = lastal.align {inherit ref;} tnpair.normal.files;
"whisper.bam" = whisper.align {inherit ref;} tnpair.normal.files;
"bwa-mem.bam" = bwa.mem {inherit ref;} tnpair.normal.files;
"bwa-mem2.bam" = bwa.mem2 {inherit ref;} tnpair.normal.files;
"minimap2-normal.bam" = minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files;
"snap-normal.bam" = snap.align {inherit ref; } tnpair.normal.files;
"${tnpair.tumour.name}.flagstat" = flagstat tnpairResult.alignments.tumour;
"hisat2-normal.bam" = hisat2.align {inherit ref;} tnpair.normal.files;
};
testNaming = linkOutputs {
kallisto = kallisto.quant {inherit ref;} (attrValues tnpair.tumour.files);
facets = facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = 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]);
lumpy = lumpy.call {} (with tnpairResult.alignments; [normal tumour]);
manta = manta.call {} (with tnpairResult.alignments; {normals = [normal tumour]; });
mantaTN = manta.call {} (with tnpairResult.alignments; {normals = [normal]; tumour = tumour;});
mantaT = manta.call {} (with tnpairResult.alignments; {tumour = 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]);
"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; };
inherit alignments;
};
in testNaming
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