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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;
glvariants = strelka.call {} (builtins.attrValues alignments);
platypusVars = platypus.call {} (builtins.attrValues alignments);
shards = pipe [
(shard.fastQPair 2)
(map (bwa.align {inherit ref;}))
] normal.files;
};
tnpairResult = processPair tnpair;
testNaming = linkDrv [
(ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets")
(ln tnpairResult.variants "strelka")
(ln tnpairResult.glvariants "strelka-gl")
(ln tnpairResult.variants.indels "strelka.indels.vcf")
(ln tnpairResult.variants.snvs "strelka.snvs.vcf")
(ln tnpairResult.glvariants.variants "strelka.gl.vcf")
(ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam")
(ln (minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files) "alignments/minimap2-normal.bam")
(ln (snap.align {inherit ref; } tnpair.normal.files) "alignments/snap-normal.bam")
(ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss")
(ln (gridss.call (with tnpairResult.alignments; [normal tumour])) "gridss2")
(ln (gridss.callAndAssemble (with tnpairResult.alignments; [normal tumour])) "gridss3")
(ln (samtools.merge {} tnpairResult.shards) "alignments/merged-shards.bam")
(ln (samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]) "alignments/merged.bam")
(ln (samtools.merge {} [(nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal)]) "alignments/merged-namesorted.bam")
(ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)) "alignments/${tnpair.tumour.name}.cram")
#(ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)) "alignments/${tnpair.normal.name}.cram")
(ln (flagstat tnpairResult.alignments.tumour) "alignments/${tnpair.tumour.name}.flagstat")
#(ln (flagstat tnpairResult.alignments.normal) "alignments/${tnpair.normal.name}.flagstat")
(ln (check-fastqc tnpair.tumour.files.input1) "fastqc/${tnpair.tumour.name}.1")
#(ln (check-fastqc tnpair.normal.files.input1) "fastqc/${tnpair.normal.name}.1")
#(ln (check-fastqc tnpair.normal.files.input2) "fastqc/${tnpair.normal.name}.2")
#(ln (check-fastqc tnpair.tumour.files.input2) "fastqc/${tnpair.tumour.name}.2")
(ln (check-fastp tnpair.tumour.files) "fastp/${tnpair.tumour.name}")
];
in testNaming
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