From 8b97c7e8f685dd3c402e172ea15ef9716b529c8e Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 18 Dec 2019 09:54:54 +1100
Subject: lumpy: init

---
 default.nix          |  1 +
 test-tnpair.nix      |  1 +
 tools/lumpy-call.nix | 40 ++++++++++++++++++++++++++++++++++++++++
 tools/lumpy.nix      |  7 +++++++
 4 files changed, 49 insertions(+)
 create mode 100644 tools/lumpy-call.nix
 create mode 100644 tools/lumpy.nix

diff --git a/default.nix b/default.nix
index a7b9c52..acf08f9 100644
--- a/default.nix
+++ b/default.nix
@@ -42,6 +42,7 @@ let
     xenomapper = callBionix ./tools/xenomapper.nix {};
     manta = callBionix ./tools/manta.nix {};
     delly = callBionix ./tools/delly.nix {};
+    lumpy = callBionix ./tools/lumpy.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 ae88549..38eb509 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -72,6 +72,7 @@ let
     "strelka.snvs.vcf" = tnpairResult.variants.snvs;
     "strelka.gl.vcf" = tnpairResult.glvariants;
     delly = delly.call {} (with tnpairResult.alignments; [normal tumour]);
+    lumpy = lumpy.call {} (with tnpairResult.alignments; [normal tumour]);
     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;});
diff --git a/tools/lumpy-call.nix b/tools/lumpy-call.nix
new file mode 100644
index 0000000..e5fb7d3
--- /dev/null
+++ b/tools/lumpy-call.nix
@@ -0,0 +1,40 @@
+{ bionix, flags ? "", faidxAttrs ? { }, indexAttrs ? { } }:
+
+inputs:
+
+with bionix;
+with lib;
+with types;
+
+let
+  getref = matchFiletype "manta-call" { bam = x: x.ref; };
+  refs = map getref inputs;
+  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 = "lumpy";
+  buildInputs = with pkgs; [ lumpy ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    ln -s ${samtools.faidx faidxAttrs ref} ref.fa.fai
+    lumpyexpress \
+      ${
+        concatMapStringsSep " " (i: "-B ${renameAndIndex i}/sample.bam") inputs
+      } \
+      ${flags} \
+      -o $out
+  '';
+  passthru.filetype = filetype.vcf { ref = ref; };
+}
diff --git a/tools/lumpy.nix b/tools/lumpy.nix
new file mode 100644
index 0000000..0894054
--- /dev/null
+++ b/tools/lumpy.nix
@@ -0,0 +1,7 @@
+{ bionix }:
+
+with bionix;
+
+{
+  call = callBionixE ./lumpy-call.nix;
+}
-- 
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