diff options
| author | Justin Bedo <cu@cua0.org> | 2019-01-14 09:47:18 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-01-14 09:47:18 +1100 |
| commit | df004c05e563a3d6e574f9b14c0939f9cd15d802 (patch) | |
| tree | 460978444507a1612b1351d1dcd73b99828c4092 | |
| parent | 5eb846d72d7f56e025a2598c3ad9c4bae7b8542a (diff) | |
cnvkit: fix annotation bug
| -rw-r--r-- | tools/cnvkit-batch.nix | 2 |
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 \ |