From 2bf74101a862d0417ccda2bafe55e0d2616d1e1a Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 15 Jan 2019 14:31:15 +1100
Subject: strelka: add germline calling

---
 tools/strelka-call.nix        |  8 +++-----
 tools/strelka-callSomatic.nix | 45 +++++++++++++++++++++++++++++++++++++++++++
 tools/strelka.nix             |  1 +
 3 files changed, 49 insertions(+), 5 deletions(-)
 create mode 100644 tools/strelka-callSomatic.nix

(limited to 'tools')

diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index 8505302..cbdcfb4 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -4,7 +4,7 @@
 , flags ? null
 }:
 
-{normal, tumour}:
+inputs:
 
 with bionix;
 with lib;
@@ -13,7 +13,6 @@ with types;
 let
   filename = path: last (splitString "/" path);
   getref = f: matchFiletype "strelka-call" { bam = x: x.ref; } f;
-  inputs = [ normal tumour ];
   refs = map getref inputs;
   ref = head refs;
 
@@ -30,9 +29,8 @@ stage {
     ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
     ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
 
-    configureStrelkaSomaticWorkflow.py \
-      --normalBam ${filename normal}.bam \
-      --tumourBam ${filename tumour}.bam \
+    configureStrelkaGermlineWorkflow.py \
+      ${concatMapStringsSep " " (i: "--bam ${filename i}.bam") inputs} \
       --ref ref.fa \
       --runDir $TMPDIR
 
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix
new file mode 100644
index 0000000..8505302
--- /dev/null
+++ b/tools/strelka-callSomatic.nix
@@ -0,0 +1,45 @@
+{ bionix
+, indexAttrs ? {}
+, bamIndexAttrs ? {}
+, flags ? null
+}:
+
+{normal, tumour}:
+
+with bionix;
+with lib;
+with types;
+
+let
+  filename = path: last (splitString "/" path);
+  getref = f: matchFiletype "strelka-call" { bam = x: x.ref; } f;
+  inputs = [ normal tumour ];
+  refs = map getref inputs;
+  ref = head refs;
+
+in
+
+assert (length (unique refs) == 1);
+
+stage {
+  name = "strelka";
+  buildInputs = with pkgs; [ strelka ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
+    ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
+    ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
+
+    configureStrelkaSomaticWorkflow.py \
+      --normalBam ${filename normal}.bam \
+      --tumourBam ${filename tumour}.bam \
+      --ref ref.fa \
+      --runDir $TMPDIR
+
+    ./runWorkflow.py \
+      -m local \
+      -j $NIX_BUILD_CORES
+
+    cp -r results $out
+   '';
+}
diff --git a/tools/strelka.nix b/tools/strelka.nix
index 47d5832..04facb9 100644
--- a/tools/strelka.nix
+++ b/tools/strelka.nix
@@ -3,5 +3,6 @@
 with bionix;
 
 {
+  callSomatic = callBionixE ./strelka-callSomatic.nix;
   call = callBionixE ./strelka-call.nix;
 }
-- 
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