From c48e7b40c82326006136463282b803eebc648df0 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 16 Dec 2019 20:43:04 +1100
Subject: manta: init

---
 default.nix          |  1 +
 test-tnpair.nix      |  3 +++
 tools/manta-call.nix | 40 ++++++++++++++++++++++++++++++++++++++++
 tools/manta.nix      |  7 +++++++
 4 files changed, 51 insertions(+)
 create mode 100644 tools/manta-call.nix
 create mode 100644 tools/manta.nix

diff --git a/default.nix b/default.nix
index 49de832..7ad804f 100644
--- a/default.nix
+++ b/default.nix
@@ -40,6 +40,7 @@ let
     snver = callBionix ./tools/snver.nix {};
     hisat2 = callBionix ./tools/hisat2.nix {};
     xenomapper = callBionix ./tools/xenomapper.nix {};
+    manta = callBionix ./tools/manta.nix {};
 
     slurm = attrs: bionix.extend (self: super: with self; rec {
       slurmDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; partition = null; slurmFlags = null; salloc = "/usr/bin/salloc"; srun = "/usr/bin/srun"; } // attrs;
diff --git a/test-tnpair.nix b/test-tnpair.nix
index f320f58..49c9bb9 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -74,6 +74,9 @@ let
     strelka-indels = tnpairResult.variants.indels;
     "strelka.snvs.vcf" = tnpairResult.variants.snvs;
     "strelka.gl.vcf" = tnpairResult.glvariants;
+    manta = manta.call {} (with tnpairResult.alignments; {normals = [normal tumour]; });
+    mantaTN = manta.call {} (with tnpairResult.alignments; {normals = [normal]; tumour = tumour;});
+    mantaT = manta.call {} (with tnpairResult.alignments; {tumour = tumour;});
     gridss = gridss.callVariants {} (with tnpairResult.alignments; [normal tumour]);
     gridss2 = gridss.call (with tnpairResult.alignments; [normal tumour]);
     gridss3 = gridss.callAndAssemble (with tnpairResult.alignments; [normal tumour]);
diff --git a/tools/manta-call.nix b/tools/manta-call.nix
new file mode 100644
index 0000000..e230a40
--- /dev/null
+++ b/tools/manta-call.nix
@@ -0,0 +1,40 @@
+{ bionix, indexAttrs ? {}, faidxAttrs ? {}, flags ? "" }:
+
+{ normals ? [], tumour ? null }:
+
+with bionix;
+with lib;
+with types;
+
+let
+  getref = matchFiletype "manta-call" { bam = x: x.ref; };
+  refs = map getref normals ++ optionals (tumour != null) [(getref tumour)];
+  ref = head refs;
+
+  renameAndIndex = f: stage {
+    name = "rename";
+    buildCommand = ''
+      mkdir $out
+      ln -s ${f} $out/sample.bam
+      ln -s ${samtools.index indexAttrs f} $out/sample.bam.bai
+    '';
+  };
+in
+
+assert (length (unique refs) == 1);
+
+stage {
+  name = "manta-call";
+  buildInputs = with pkgs; [ manta strace ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
+    configManta.py ${optionalString (normals != null) (concatMapStringsSep " " (n: "--bam=${renameAndIndex n}/sample.bam") normals)} \
+      ${optionalString (tumour != null) "--tumourBam=${renameAndIndex tumour}/sample.bam"} \
+      --runDir=$TMPDIR \
+      --referenceFasta=ref.fa \
+      ${flags}
+    ./runWorkflow.py
+    cp -r results $out
+  '';
+}
diff --git a/tools/manta.nix b/tools/manta.nix
new file mode 100644
index 0000000..aa8b762
--- /dev/null
+++ b/tools/manta.nix
@@ -0,0 +1,7 @@
+{ bionix }:
+
+with bionix;
+
+{
+  call = callBionix ./manta-call.nix;
+}
-- 
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