strelka: rewrite to use multiple outputs

4 files changed, 22 insertions, 39 deletions

diff --git a/test-tnpair.nix b/test-tnpair.nix
index 2ea93ae..4d6a794 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -51,9 +51,9 @@ let
     (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets")
     (ln tnpairResult.variants "strelka")
     (ln tnpairResult.glvariants "strelka-gl")
-    (ln (strelka.indels tnpairResult.variants) "strelka.indels.vcf")
-    (ln (strelka.snvs tnpairResult.variants) "strelka.snvs.vcf")
-    (ln (strelka.variants tnpairResult.glvariants) "strelka.gl.vcf")
+    (ln tnpairResult.variants.indels "strelka.indels.vcf")
+    (ln tnpairResult.variants.snvs "strelka.snvs.vcf")
+    (ln tnpairResult.glvariants.variants "strelka.gl.vcf")
     (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam")
     (ln (minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files) "alignments/minimap2-normal.bam")
     (ln (snap.align {inherit ref; } tnpair.normal.files) "alignments/snap-normal.bam")
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index bc1e202..dc07291 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -20,9 +20,11 @@ in
 
 assert (length (unique refs) == 1);
 
-stage {
+let
+out = stage {
   name = "strelka-call";
   buildInputs = with pkgs; [ strelka ];
+  outputs = [ "out" "variants" ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
@@ -48,8 +50,12 @@ stage {
       sed -i '/^##fileDate/d' $g
       sed -i '/^##startTime/d' $g
     done
+    mv variants.vcf $variants
+    ln -s $variants variants.vcf
     mkdir $out
     cp -r * $out
   '';
   passthru.multicore = true;
-}
+};
+ft = {filetype = types.filetype.vcf {ref = ref;};};
+in out // { variants = out.variants // ft; }
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix
index cf4b414..cce6243 100644
--- a/tools/strelka-callSomatic.nix
+++ b/tools/strelka-callSomatic.nix
@@ -21,9 +21,12 @@ in
 
 assert (length (unique refs) == 1);
 
-stage {
+let
+
+out = stage {
   name = "strelka-callSomatic";
   buildInputs = with pkgs; [ strelka ];
+  outputs = [ "out" "indels" "snvs" ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
@@ -50,8 +53,14 @@ stage {
       sed -i '/^##fileDate/d' $g
       sed -i '/^##startTime/d' $g
     done
+    mv somatic.indels.vcf $indels
+    ln -s $indels somatic.indels.vcf
+    mv somatic.snvs.vcf $snvs
+    ln -s $snvs somatic.snvs.vcf
     mkdir $out
     cp -r * $out
   '';
   passthru.multicore = true;
-}
+};
+ft = {filetype = types.filetype.vcf {ref = ref;};};
+in out // { indels = out.indels // ft; snvs = out.snvs // ft;}
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;};
-  };
 }