diff options
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/hatchet-call.nix | 257 |
1 files changed, 132 insertions, 125 deletions
diff --git a/tools/hatchet-call.nix b/tools/hatchet-call.nix index c99e664..55414fe 100644 --- a/tools/hatchet-call.nix +++ b/tools/hatchet-call.nix @@ -1,131 +1,138 @@ -{ 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" +{ + 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; + { + 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 ${script} + ''; in - linkOutputs { - "vcf.bgz" = bz; - "vcf.bgz.tbi" = samtools.tabix { } bz; - }; - - getSN = - let - script = pkgs.writeText "getSN.awk" '' - BEGIN{ - FS=":" - RS="[ \t\n]" + stage + ({ + name = "HATCHet"; + buildInputs = + [hatchet.app getSN pkgs.samtools pkgs.bcftools] + ++ ( + if gurobiLicense == null + then [pkgs.cbc] + else [pkgs.gurobi] + ); + buildCommand = '' + # Get tumour names + names="${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; } - $1=="SM"{print $2; exit} - ''; - in - pkgs.writeShellScriptBin "getSN" '' - exec samtools view -H "$1" | awk -f ${script} - ''; - -in -stage - ({ - name = "HATCHet"; - buildInputs = [ hatchet.app getSN pkgs.samtools pkgs.bcftools ] ++ optional (gurobiLicense == null) pkgs.cbc; - buildCommand = '' - # Get tumour names - names="${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"; - })) + // ( + if gurobiLicense != null + then { + GRB_LICENSE_FILE = gurobiLicense; + HATCHET_COMPUTE_CN_SOLVER = "gurobi"; + } + else { + HATCHET_COMPUTE_CN_SOLVER = "cbc"; + } + )) |