strelka: rewrite to use multiple outputs

1 files changed, 0 insertions, 32 deletions

diff --git a/tools/strelka.nix b/tools/strelka.nix
index d3068b5..16f4a2b 100644
--- a/tools/strelka.nix
+++ b/tools/strelka.nix
@@ -12,36 +12,4 @@ with types;
   Type: call :: {...} -> [input] -> results
   */
   call = callBionixE ./strelka-call.nix;
-  /* Extract VCF file from results
-  Type: variants :: results -> vcf
-  */
-  variants =
-    # result of call
-    drv: stage {
-    name = "strelka-call-variants";
-    buildCommand = ''
-      ln -s ${drv}/variants/variants.vcf $out
-    '';
-    passthru.filetype = filetype.vcf {ref=ref;};
-  };
-  /* Extract indels from somatic results
-  Type: indels :: somatic results -> vcf
-  */
-  indels =
-    # result of callSomatic
-    drv: stage {
-    name = "strelka-callVariants-indels";
-    buildCommand = "ln -s ${drv}/variants/somatic.indels.vcf $out";
-    passthru.filetype = filetype.vcf {ref = ref;};
-  };
-  /* Extract SNVs from somatic results
-  Type: snvs :: somatic results -> vcf
-  */
-  snvs =
-    # result of callSomatic
-    drv: stage {
-    name = "strelka-callVariants-snvs";
-    buildCommand = "ln -s ${drv}/variants/somatic.snvs.vcf $out";
-    passthru.filetype = filetype.vcf {ref = ref;};
-  };
 }