From d9223958d2d83a936719694db63c4777a8dde274 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 16 Jan 2019 11:14:00 +1100
Subject: strelka: split out vcfs

---
 tools/strelka-call.nix        | 17 +++++++++++++----
 tools/strelka-callSomatic.nix | 34 ++++++++++++++++++++++++----------
 2 files changed, 37 insertions(+), 14 deletions(-)

diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index cbdcfb4..e90bdfd 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -16,12 +16,14 @@ let
   refs = map getref inputs;
   ref = head refs;
 
+  drv = bionix.strelka.call {inherit indexAttrs bamIndexAttrs flags;} inputs;
+
 in
 
 assert (length (unique refs) == 1);
 
 stage {
-  name = "strelka";
+  name = "strelka-call";
   buildInputs = with pkgs; [ strelka ];
   buildCommand = ''
     ln -s ${ref} ref.fa
@@ -30,14 +32,21 @@ stage {
     ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
 
     configureStrelkaGermlineWorkflow.py \
-      ${concatMapStringsSep " " (i: "--bam ${filename i}.bam") inputs} \
+    ${concatMapStringsSep " " (i: "--bam ${filename i}.bam") inputs} \
       --ref ref.fa \
       --runDir $TMPDIR
 
     ./runWorkflow.py \
       -m local \
-      -j $NIX_BUILD_CORES
+      -j $NIX_BUILD_CORES 2>&1
 
     cp -r results $out
-   '';
+  '';
+  passthru.variants = stage {
+    name = "strelka-call-variants";
+    buildCommand = ''
+      ln -s ${drv}/variants/variants.vcf.gz $out
+    '';
+    passthru.filetype = filetype.gz (filetype.vcf {ref=ref;});
+  };
 }
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix
index 8505302..888e589 100644
--- a/tools/strelka-callSomatic.nix
+++ b/tools/strelka-callSomatic.nix
@@ -12,18 +12,20 @@ with types;
 
 let
   filename = path: last (splitString "/" path);
-  getref = f: matchFiletype "strelka-call" { bam = x: x.ref; } f;
+  getref = f: matchFiletype "strelka-callSomatic" { bam = x: x.ref; } f;
   inputs = [ normal tumour ];
   refs = map getref inputs;
   ref = head refs;
 
+  drv = bionix.strelka.callSomatic {inherit indexAttrs bamIndexAttrs flags;} {inherit normal tumour;};
+
 in
 
 assert (length (unique refs) == 1);
 
 stage {
-  name = "strelka";
-  buildInputs = with pkgs; [ strelka ];
+  name = "strelka-callSomatic";
+  buildInputs = with pkgs; [ strelka gzip ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
@@ -31,15 +33,27 @@ stage {
     ${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
+    --normalBam ${filename normal}.bam \
+    --tumourBam ${filename tumour}.bam \
+    --ref ref.fa \
+    --runDir $TMPDIR
 
     ./runWorkflow.py \
-      -m local \
-      -j $NIX_BUILD_CORES
+    -m local \
+    -j $NIX_BUILD_CORES
 
     cp -r results $out
-   '';
+  '';
+  passthru = {
+    indels = stage {
+      name = "strelka-callVariants-indels";
+      buildCommand = "ln -s ${drv}/variants/somatic.indels.vcf.gz $out";
+      passthru.filetype = filetype.gz (filetype.vcf {ref = ref;});
+    };
+    snvs = stage {
+      name = "strelka-callVariants-snvs";
+      buildCommand = "ln -s ${drv}/variants/somatic.snvs.vcf.gz $out";
+      passthru.filetype = filetype.gz (filetype.vcf {ref = ref;});
+    };
+  };
 }
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