Don't bother compressing filtered FASTAs
These should be small enough, it isn't worth the extra effort/complexity
to compress.
@@ -594,7 +594,6 @@ rule filter:
min_date = lambda wildcards: _get_filter_value(wildcards, "min_date"),
ambiguous = lambda wildcards: f"--exclude-ambiguous-dates-by {_get_filter_value(wildcards, 'exclude_ambiguous_dates_by')}" if _get_filter_value(wildcards, "exclude_ambiguous_dates_by") else "",
date = (date.today() + datetime.timedelta(days=1)).strftime("%Y-%m-%d"),
- intermediate_output=lambda wildcards, output: Path(output.sequences).with_suffix("")
resources:
# Memory use scales primarily with the size of the metadata file.
mem_mb=500
@@ -611,8 +610,7 @@ rule filter:
--exclude {input.exclude} \
--exclude-where {params.exclude_where}\
--min-length {params.min_length} \
- --output {params.intermediate_output} 2>&1 | tee {log};
- xz -2 {params.intermediate_output}
+ --output {output.sequences} 2>&1 | tee {log};
"""
if "run_pangolin" in config and config["run_pangolin"]:
