strelka: refactor vcf extraction

3 files changed, 27 insertions, 32 deletions

diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index e90bdfd..1162558 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -16,14 +16,12 @@ 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-call";
+  name = "strelka";
   buildInputs = with pkgs; [ strelka ];
   buildCommand = ''
     ln -s ${ref} ref.fa
@@ -32,7 +30,7 @@ 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
 
@@ -42,11 +40,4 @@ stage {
 
     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 888e589..6d379f9 100644
--- a/tools/strelka-callSomatic.nix
+++ b/tools/strelka-callSomatic.nix
@@ -17,14 +17,12 @@ let
   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-callSomatic";
+  name = "strelka";
   buildInputs = with pkgs; [ strelka gzip ];
   buildCommand = ''
     ln -s ${ref} ref.fa
@@ -33,27 +31,15 @@ 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;});
-    };
-  };
 }
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;});
+  };
 }