1 files changed, 130 insertions, 0 deletions
diff --git a/tools/hatchet-call.nix b/tools/hatchet-call.nix
new file mode 100644
index 0000000..a3bd5ca
--- /dev/null
+++ b/tools/hatchet-call.nix
@@ -0,0 +1,130 @@
+{ 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 ${script}
+    '';
+
+in
+stage
+  ({
+    name = "HATCHet";
+    buildInputs = [ hatchet.app getSN pkgs.samtools pkgs.bcftools ] ++ optional (gurobiLicense == null) pkgs.cbc;
+    buildCommand = ''
+      # Get tumour names
+      names="${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;
+  } else {
+    HATCHET_COMPUTE_CN_SOLVER = "cbc";
+  }))