blob: ef2af1bdd7d536d8cff1eb4258a9a5a4aee3555f (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
|
with (import <nixpkgs> {});
with (import <bionix> {});
with lib;
let
ref = ./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 {};
callVariants = strelka.call { inherit ref; };
tnpair = { tumour = {name = "mysample1"; files = {input1 = ./example/sample1-1.fq; input2 = ./example/sample1-2.fq;};};
normal = {name = "mysample2"; files = {input1 = ./example/sample2-1.fq; input2 = ./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 ${tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.bam
ln -s ${tnpairResult.alignments.normal} $out/alignments/${tnpair.normal.name}.bam
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
|
