Remove unnecessary rule to aggregate exclude files
Now that augur filter supports multiple input files for both include and
exclude arguments, we can pass these filenames directly to the filter
rule instead of aggregating the files in an earlier rule.
@@ -165,18 +165,6 @@ def _collect_exclusion_files(wildcards):
exclude_files.append(_get_path_for_input("to-exclude", wildcards.origin))
return exclude_files
-rule exclude_file:
- input:
- _collect_exclusion_files
- output:
- "results/exclude{origin}.txt"
- benchmark:
- "benchmarks/exclude_file{origin}.txt"
- shell:
- """
- cat {input} > {output}
- """
-
rule mask:
message:
"""
@@ -222,7 +210,7 @@ rule filter:
metadata = "results/sanitized_metadata{origin}.tsv",
# TODO - currently the include / exclude files are not input (origin) specific, but this is possible if we want
include = config["files"]["include"],
- exclude = rules.exclude_file.output
+ exclude = _collect_exclusion_files,
output:
sequences = "results/filtered{origin}.fasta"
log:
