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{
bionix,
gurobiLicense ? null,
count_reads ? true,
genotype_snps ? true,
count_alleles ? true,
combine_counts ? true,
cluster_bins ? true,
plot_bins ? true,
compute_cn ? true,
plot_cn ? true,
size ? "50kb",
mincov ? 8,
maxcov ? 300,
snps,
phase ? "None",
diploidbaf ? 0.08,
tolerancerdr ? 0.15,
tolerancebaf ? 0.04,
sizethreshold ? 0.01,
figsize ? "6,3",
clones ? [2 6],
seeds ? 400,
minprop ? 0.03,
diploidcmax ? 6,
tetraploidcmax ? 12,
ghostprop ? 0.35,
limitinc ? 0.6,
blocklength ? "50kb",
}:
with bionix;
with lib;
with types;
{
normal,
tumours,
}: let
getRef = matchFiletype "hatchet" {bam = {ref, ...}: ref;};
in
assert all (x: getRef normal == getRef x) tumours; let
ref = getRef normal;
ini = pkgs.writeText "hatchet.ini" (generators.toINI {} {
run = {
inherit count_reads genotype_snps count_alleles combine_counts cluster_bins plot_bins compute_cn plot_cn;
reference = "${lnRef ref}/ref.fa";
normal = "${lnBam normal}/input.bam";
bams = concatMapStringsSep " " (x: "${lnBam x}/input.bam") tumours;
samples = "@SAMPLES@";
output = "./out";
processes = "@PROCESSES@";
};
count_reads = {inherit size;};
genotype_snps = {
inherit mincov maxcov;
snps = "${lnVcfBz snps}/vcf.bgz";
};
count_alleles = {inherit mincov maxcov;};
combine_counts = {inherit blocklength phase;};
cluster_bins = {inherit diploidbaf tolerancerdr tolerancebaf;};
plot_bins = {inherit sizethreshold figsize;};
compute_cn = {
inherit seeds minprop diploidcmax tetraploidcmax ghostprop limitinc;
clones = concatMapStringsSep "," builtins.toString clones;
};
});
lnRef = ref:
linkOutputs {
"ref.fa" = ref;
"ref.fa.fai" = samtools.faidx {} ref;
"ref.dict" = samtools.dict {} ref;
};
lnBam = bam:
linkOutputs {
"input.bam" = bam;
"input.bam.bai" = samtools.index {} bam;
};
lnVcfBz = vcf: let
bz = compression.bgzip {} vcf;
in
linkOutputs {
"vcf.bgz" = bz;
"vcf.bgz.tbi" = samtools.tabix {} bz;
};
getSN = let
script = pkgs.writeText "getSN.awk" ''
BEGIN{
FS=":"
RS="[ \t\n]"
}
$1=="SM"{print $2; exit}
'';
in
pkgs.writeShellScriptBin "getSN" ''
exec samtools view -H "$1" | awk -f ${script}
'';
in
stage
({
name = "HATCHet";
buildInputs =
[hatchet.app getSN pkgs.samtools pkgs.bcftools]
++ (
if gurobiLicense == null
then [pkgs.cbc]
else [pkgs.gurobi]
);
buildCommand = ''
# Get tumour names
names="${concatMapStringsSep " " (x: "$(getSN ${x})") tumours}"
# macro substitute ini file
substitute ${ini} hatchet.ini \
--replace "@PROCESSES@" "$NIX_BUILD_CORES" \
--replace "@SAMPLES@" "$names"
hatchet run hatchet.ini
cp -r out $out
'';
passthru.multicore = true;
}
// (
if gurobiLicense != null
then {
GRB_LICENSE_FILE = gurobiLicense;
HATCHET_COMPUTE_CN_SOLVER = "gurobi";
}
else {
HATCHET_COMPUTE_CN_SOLVER = "cbc";
}
))
|
