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authorJustin Bedo <cu@cua0.org>2019-01-14 09:47:18 +1100
committerJustin Bedo <cu@cua0.org>2019-01-14 09:47:18 +1100
commitdf004c05e563a3d6e574f9b14c0939f9cd15d802 (patch)
tree460978444507a1612b1351d1dcd73b99828c4092
parent5eb846d72d7f56e025a2598c3ad9c4bae7b8542a (diff)
cnvkit: fix annotation bug
-rw-r--r--tools/cnvkit-batch.nix2
1 files changed, 1 insertions, 1 deletions
diff --git a/tools/cnvkit-batch.nix b/tools/cnvkit-batch.nix
index 67eaac3..6fb97a4 100644
--- a/tools/cnvkit-batch.nix
+++ b/tools/cnvkit-batch.nix
@@ -28,7 +28,7 @@ stage {
ln -s ${samtools.faidx indexAttrs ref} ref.fa.fai
cnvkit.py batch ${concatStringsSep " " tumours} \
${optionalString (normals != []) ("-n " + concatStringsSep " " normals)} \
- ${optionalString (annotations != null) annotations} \
+ ${optionalString (annotations != null) "--annotate ${annotations}"} \
${if targets != null then "--targets ${targets}" else "-m wgs"} \
-f ref.fa \
-p $NIX_BUILD_CORES \