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| author | Justin Bedo <cu@cua0.org> | 2018-09-27 15:41:09 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-09-27 15:41:09 +1000 |
| commit | a75e95881c49cfa52cc47c27a4980b2381cc0fbf (patch) | |
| tree | 69055aa697af0d1bdc87f879ae62a00ed70b8338 /tools/bwa-index.nix | |
| parent | 0d239a650a60a14e4820f73a02e3064e050b2398 (diff) | |
Allow flag passing to bwa index
Diffstat (limited to 'tools/bwa-index.nix')
| -rw-r--r-- | tools/bwa-index.nix | 3 |
1 files changed, 2 insertions, 1 deletions
diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix index b5e3779..3329221 100644 --- a/tools/bwa-index.nix +++ b/tools/bwa-index.nix @@ -1,6 +1,7 @@ { stdenv , lib , bwa +, flags ? null }: ref: @@ -12,7 +13,7 @@ stdenv.mkDerivation { buildInputs = [ bwa ]; buildCommand = '' ln -s ${ref} ref.fa - bwa index ref.fa + bwa index ${optionalString (flags != null) flags} ref.fa mkdir $out mv ref.fa.* $out grep '^>[^ \t]*_alt$' ref.fa | tr -d '^>' > $out/idxbase.alt || true |