diff options
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/bwa-index.nix | 4 |
1 files changed, 3 insertions, 1 deletions
diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix index 17b651f..65d9bd5 100644 --- a/tools/bwa-index.nix +++ b/tools/bwa-index.nix @@ -1,5 +1,6 @@ { bionix , flags ? null +, altRegex ? "^>.*_alt$" }: ref: @@ -18,6 +19,7 @@ stage { bwa index ${optionalString (flags != null) flags} ref.fa mkdir $out mv ref.fa.* $out - grep '^>[^ \t]*_alt$' ref.fa | tr -d '^>' > $out/idxbase.alt || true + grep -P '${altRegex}' ref.fa | tr -d '^>' > $out/idxbase.alt || true ''; + stripStorePaths = false; } |