fix: don't compress mask output, augur tree can't handle it
@@ -561,7 +561,7 @@ rule mask:
input:
alignment = rules.build_align.output.alignment
output:
- alignment = "results/{build_name}/masked.fasta.xz"
+ alignment = "results/{build_name}/masked.fasta"
log:
"logs/mask_{build_name}.txt"
benchmark:
@@ -579,7 +579,7 @@ rule mask:
--mask-from-end {params.mask_from_end} \
--mask-sites {params.mask_sites} \
--mask-terminal-gaps \
- --output /dev/stdout | xz -c -2 > {output.alignment} 2> {log}
+ --output {output.alignment} 2> {log}
"""
rule compress_build_align:
