1 files changed, 9 insertions, 4 deletions
diff --git a/tools/compression-gzip.nix b/tools/compression-gzip.nix
index 0229b94..80fb9f4 100644
--- a/tools/compression-gzip.nix
+++ b/tools/compression-gzip.nix
@@ -1,12 +1,17 @@
-{ bionix }:
+{ bionix, block ? false, flags ? "" }:
 
 with bionix;
+with types;
 
 input:
 
 stage {
   name = "gzip";
-  buildInputs = with pkgs; [ gzip ];
-  buildCommand = "gzip < ${input} > $out";
-  passthru.filetype = filetype.gzip input.filetype;
+  buildInputs = with pkgs; [ (if block then htslib else gzip) ];
+  buildCommand =
+    if block then
+      "bgzip -c ${flags} ${input} > $out"
+    else
+      "gzip ${flags} < ${input} > $out";
+  passthru.filetype = (if block then filetype.bgz else filetype.gz) input.filetype;
 }