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ONT_pilot_gitlab
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51625908
Commit
51625908
authored
4 years ago
by
Valentina Galata
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init: allow null value for host_refs for bbmap in config
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d73960ca
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workflow/rules/init.smk
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@@ -29,7 +29,7 @@ if config["data"]["metat"]["sr"]["r1"] and config["data"]["metat"]["sr"]["r2"]:
NO_BASECALLING = config["data"]["metag"]["ont"]["fastq"] and os.path.exists(config["data"]["metag"]["ont"]["fastq"])
# Whether host contamination has to be removed - only if host references are given
NO_HOST_FILTERING = len(config["bbmap"]["host_refs"].keys()) == 0
NO_HOST_FILTERING =
config["bbmap"]["host_refs"] is None or
len(config["bbmap"]["host_refs"].keys()) == 0
# Assemblers and read types
META_TYPES = ["metag"]
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