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-rw-r--r--tools/strelka-call.nix10
-rw-r--r--tools/strelka-callSomatic.nix11
2 files changed, 7 insertions, 14 deletions
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