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-rw-r--r--tools/strelka-callSomatic.nix4
1 files changed, 3 insertions, 1 deletions
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix
index fd58d33..b409344 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 = [ "indels" "snvs" ];
+ outputs = [ "out" "indels" "snvs" ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
@@ -56,6 +56,8 @@ out = stage {
done
mv somatic.indels.vcf $indels
mv somatic.snvs.vcf $snvs
+
+ ln -s $snvs $out
'';
passthru.multicore = true;
passthru.filetype = types.filetype.vcf {ref = ref;};