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-rw-r--r--tools/bwa-index.nix4
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;
}