Run xz outside python.
xopen+lzma has performance issues as it does not support passing compression levels to py-lzma.
@@ -356,7 +356,8 @@ rule combine_sequences_for_subsampling:
| python3 scripts/combine-and-dedup-fastas.py \
--input /dev/stdin \
{params.warn_about_duplicates} \
- --output {output}
+ --output /dev/stdout \
+ | xz -2 > {output}
"""
rule index_sequences:
