strelka: refactor vcf extraction

1 files changed, 18 insertions, 0 deletions

diff --git a/tools/strelka.nix b/tools/strelka.nix
index 04facb9..9a8f1aa 100644
--- a/tools/strelka.nix
+++ b/tools/strelka.nix
@@ -1,8 +1,26 @@
 { bionix }:
 
 with bionix;
+with types;
 
 {
   callSomatic = callBionixE ./strelka-callSomatic.nix;
   call = callBionixE ./strelka-call.nix;
+  variants = drv: stage {
+    name = "strelka-call-variants";
+    buildCommand = ''
+      ln -s ${drv}/variants/variants.vcf.gz $out
+    '';
+    passthru.filetype = filetype.gz (filetype.vcf {ref=ref;});
+  };
+  indels = drv: stage {
+    name = "strelka-callVariants-indels";
+    buildCommand = "ln -s ${drv}/variants/somatic.indels.vcf.gz $out";
+    passthru.filetype = filetype.gz (filetype.vcf {ref = ref;});
+  };
+  snvs = drv: stage {
+    name = "strelka-callVariants-snvs";
+    buildCommand = "ln -s ${drv}/variants/somatic.snvs.vcf.gz $out";
+    passthru.filetype = filetype.gz (filetype.vcf {ref = ref;});
+  };
 }