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Remove GTDBtk from Aviary fast #122

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Jun 10, 2024
Merged

Remove GTDBtk from Aviary fast #122

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11 changes: 7 additions & 4 deletions binchicken/binchicken.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1145,7 +1145,7 @@ def add_aviary_options(argument_group):
default_assembly_strategy = DYNAMIC_ASSEMBLY_STRATEGY
argument_group.add_argument("--assembly-strategy", help=f"Assembly strategy to use with Aviary. [default: {default_assembly_strategy}; attempts metaspades and if fails, switches to megahit]",
default=default_assembly_strategy, choices=[DYNAMIC_ASSEMBLY_STRATEGY, METASPADES_ASSEMBLY, MEGAHIT_ASSEMBLY])
argument_group.add_argument("--aviary-gtdbtk-db", help="Path to GTDB-Tk database directory for Aviary. [default: use path from GTDBTK_DATA_PATH env variable]")
argument_group.add_argument("--aviary-gtdbtk-db", help=f"Path to GTDB-Tk database directory for Aviary. Only required if --aviary-speed is set to {COMPREHENSIVE_AVIARY_MODE} [default: use path from GTDBTK_DATA_PATH env variable]")
argument_group.add_argument("--aviary-checkm2-db", help="Path to CheckM2 database directory for Aviary. [default: use path from CHECKM2DB env variable]")
aviary_assemble_default_cores = 64
argument_group.add_argument("--aviary-assemble-cores", type=int, help=f"Maximum number of cores for Aviary assemble to use. [default: {aviary_assemble_default_cores}]",
Expand Down Expand Up @@ -1297,8 +1297,8 @@ def add_coassemble_arguments(parser):

build_parser = main_parser.new_subparser("build", "Create dependency conda environments")
build_parser.add_argument("--singlem-metapackage", help="SingleM metapackage")
build_parser.add_argument("--gtdbtk-db", help="GTDBtk release database")
build_parser.add_argument("--checkm2-db", help="CheckM2 database")
build_parser.add_argument(f"--gtdbtk-db", help="GTDBtk release database (Only required if --aviary-speed is set to {COMPREHENSIVE_AVIARY_MODE})")
tmp_default = "/tmp"
build_parser.add_argument("--set-tmp-dir", help=f"Set temporary directory [default: {tmp_default}]", default=tmp_default)
build_parser.add_argument("--skip-aviary-envs", help="Do not install Aviary subworkflow environments", action="store_true")
Expand Down Expand Up @@ -1382,8 +1382,11 @@ def coassemble_argument_verification(args, iterate=False):
else:
if args.num_coassembly_samples > args.max_recovery_samples:
raise Exception("Max recovery samples (--max-recovery-samples) must be greater than or equal to number of coassembly samples (--num-coassembly-samples)")
if args.run_aviary and not (args.aviary_gtdbtk_db and args.aviary_checkm2_db):
raise Exception("Run Aviary (--run-aviary) requires paths to GTDB-Tk and CheckM2 databases to be provided (--aviary-gtdbtk-db or GTDBTK_DATA_PATH and --aviary-checkm2-db or CHECKM2DB)")
if args.run_aviary:
if args.aviary_speed == FAST_AVIARY_MODE and not args.aviary_checkm2_db:
raise Exception("Run Aviary (--run-aviary) fast mode requires path to CheckM2 databases to be provided (--aviary-checkm2-db or CHECKM2DB)")
if args.aviary_speed != FAST_AVIARY_MODE and not (args.aviary_gtdbtk_db and args.aviary_checkm2_db):
raise Exception("Run Aviary (--run-aviary) comprehensive mode requires paths to GTDB-Tk and CheckM2 databases to be provided (--aviary-gtdbtk-db or GTDBTK_DATA_PATH and --aviary-checkm2-db or CHECKM2DB)")
if args.cluster_submission and not args.snakemake_profile:
logging.warning("The arg `--cluster-submission` is only a flag and cannot activate cluster submission alone. Please see `--snakemake-profile` for cluster submission.")
if (args.sample_query or args.sample_query_list or args.sample_query_dir) and args.taxa_of_interest and args.assemble_unmapped:
Expand Down
2 changes: 1 addition & 1 deletion binchicken/workflow/coassemble.smk
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Expand Up @@ -743,7 +743,7 @@ rule aviary_recover:
checkm2 = config["aviary_checkm2"],
conda_prefix = config["conda_prefix"] if config["conda_prefix"] else ".",
singlem_metapackage = config["singlem_metapackage"],
fast = "--skip-singlem --skip-abundances --refinery-max-iterations 0" if config["aviary_speed"] == FAST_AVIARY_MODE else "",
fast = "--binning-only --refinery-max-iterations 0" if config["aviary_speed"] == FAST_AVIARY_MODE else "",
snakemake_profile = f"--snakemake-profile {config['snakemake_profile']}" if config["snakemake_profile"] else "",
cluster_retries = f"--cluster-retries {config['cluster_retries']}" if config["cluster_retries"] else "",
tmpdir = f"TMPDIR={config['tmpdir']}" if config["tmpdir"] else "",
Expand Down
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