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authorJustin Bedo <cu@cua0.org>2020-10-13 08:39:36 +1100
committerJustin Bedo <cu@cua0.org>2020-10-13 08:39:36 +1100
commit2e348fecd73df140c95089ad0304fd93088721f7 (patch)
tree3d55f5e14d3b6ad810b57516a41c9cf15068d126
parent9cf1724895f001c625fba37d78f517acb6938e07 (diff)
mutect: fix app expression and tag output as vcf
-rw-r--r--tools/mutect-app.nix2
-rw-r--r--tools/mutect-call.nix1
2 files changed, 2 insertions, 1 deletions
diff --git a/tools/mutect-app.nix b/tools/mutect-app.nix
index 02c4f51..ca78d34 100644
--- a/tools/mutect-app.nix
+++ b/tools/mutect-app.nix
@@ -19,7 +19,7 @@ in stdenv.mkDerivation rec {
sha256 = "1pq7iv720bp970qsyyshwk98xdb7naw566y6gk9cpj6bmm08z9v3";
};
- buildInputs = [ makeWrapper jre unzip ];
+ buildInputs = [ makeWrapper unzip ];
unpackPhase = ''
unzip $src -d $TMPDIR
diff --git a/tools/mutect-call.nix b/tools/mutect-call.nix
index e2fe3a1..e98ba4b 100644
--- a/tools/mutect-call.nix
+++ b/tools/mutect-call.nix
@@ -38,4 +38,5 @@ stage {
--input_file:tumour tumour.bam \
--out $out
'';
+ passthru.filetype = types.filetype.vcf { inherit ref; };
}