From 233c5f9a09ba82e94b042ac22462dcdfa8ffbae2 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 6 Sep 2019 10:12:20 +1000
Subject: strelka: change outputs and tagging

This resolves an issue where overriding the strelka derivations would
lose the filetype tags.
---
 tools/strelka-call.nix        | 10 +++-------
 tools/strelka-callSomatic.nix | 11 ++++-------
 2 files changed, 7 insertions(+), 14 deletions(-)

(limited to 'tools')

diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index dc07291..a37c2aa 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -24,7 +24,6 @@ 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
@@ -50,12 +49,9 @@ out = 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
+    mv variants.vcf $out
   '';
   passthru.multicore = true;
+  passthru.filetype = types.filetype.vcf {ref = ref;};
 };
-ft = {filetype = types.filetype.vcf {ref = ref;};};
-in out // { variants = out.variants // ft; }
+in out
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix
index cce6243..ec57b8c 100644
--- a/tools/strelka-callSomatic.nix
+++ b/tools/strelka-callSomatic.nix
@@ -26,7 +26,7 @@ let
 out = stage {
   name = "strelka-callSomatic";
   buildInputs = with pkgs; [ strelka ];
-  outputs = [ "out" "indels" "snvs" ];
+  outputs = [ "indels" "snvs" ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
@@ -54,13 +54,10 @@ out = stage {
       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;
+  passthru.filetype = types.filetype.vcf {ref = ref;};
 };
-ft = {filetype = types.filetype.vcf {ref = ref;};};
-in out // { indels = out.indels // ft; snvs = out.snvs // ft;}
+
+in out
-- 
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