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Allow a list of sequence exclusion files, instead of just one #977

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Allow a list of sequence exclusion files, instead of just one #977

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10 changes: 7 additions & 3 deletions workflow/snakemake_rules/main_workflow.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -559,12 +559,16 @@ rule diagnostic:

def _collect_exclusion_files(wildcards):
# This rule creates a per-input exclude file for `rule filter`. This file contains one or both of the following:
# (1) a config-defined exclude file
# (1) a config-defined exclude file or list of such files
# (2) a dynamically created file (`rule diagnostic`) which scans the alignment for potential errors
# The second file is optional - it may be opted out via config → skip_diagnostics
exclude = config["files"]["exclude"]
if type(exclude) is not list:
exclude = [ exclude ]
if config["filter"].get("skip_diagnostics", False):
return [ config["files"]["exclude"] ]
return [ config["files"]["exclude"], f"results/{wildcards.build_name}/excluded_by_diagnostics.txt" ]
return exclude
else:
return exclude + [f"results/{wildcards.build_name}/excluded_by_diagnostics.txt"]

rule mask:
message:
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