strelka: split out vcfs

1 files changed, 24 insertions, 10 deletions

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;});
+    };
+  };
 }