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with (import <nixpkgs> {});
with lib;
let
bionix = (import <bionix> {}).extend (self: super: with self; {
bwa = with super.bwa; {
align = align;
index = def index { flags = "-a is"; };
};
});
in
with bionix;
let
fetchlocal = path: stdenv.mkDerivation {
name = baseNameOf path;
buildCommand = "ln -s ${path} $out";
};
fetchfq = attrs: types.tagFiletype (types.filetype.fq {}) (fetchlocal attrs);
fetchfa = attrs: types.tagFiletype (types.filetype.fa {}) (fetchlocal attrs);
alignWithRG = rg: bwa.align { ref = fetchfa ./example/ref.fa; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
sort = samtools.sort {};
flagstat = samtools.flagstat {};
check = fastqc.check {};
callVariants = strelka.call {};
tnpair = {
tumour = {name = "mysample1"; files = {
input1 = fetchfq ./example/sample1-1.fq;
input2 = fetchfq ./example/sample1-2.fq;
};
};
normal = {name = "mysample2"; files = {
input1 = fetchfq ./example/sample2-1.fq;
input2 = fetchfq ./example/sample2-1.fq;
};
};
};
processPair = { tumour, normal }: rec {
alignments = mapAttrs (_: x: sort (alignWithRG x.name x.files)) { inherit normal tumour; };
variants = callVariants alignments;
};
tnpairResult = processPair tnpair;
testNaming = stdenv.mkDerivation {
name = "test-naming";
buildCommand = ''
mkdir $out
ln -s ${tnpairResult.variants} $out/strelka
mkdir $out/alignments
ln -s ${gridss.callVariants {} (with tnpairResult.alignments; [tumour])} $out/gridss
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
ln -s ${flagstat tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.flagstat
ln -s ${flagstat tnpairResult.alignments.normal} $out/alignments/${tnpair.normal.name}.flagstat
mkdir $out/fastqc
ln -s ${check tnpair.tumour.files.input1} $out/fastqc/${tnpair.tumour.name}.1
ln -s ${check tnpair.tumour.files.input2} $out/fastqc/${tnpair.tumour.name}.2
ln -s ${check tnpair.normal.files.input1} $out/fastqc/${tnpair.normal.name}.1
ln -s ${check tnpair.normal.files.input2} $out/fastqc/${tnpair.normal.name}.2
'';
};
in testNaming
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