bactopia-scaffold

Scaffold Bactopia components from bioconda/conda-forge packages.

Usage

bactopia-scaffold COMMAND [OPTIONS]

Subcommands

Command	Description
bactopia-scaffold lookup	Look up package info from Anaconda and check for existing components.
bactopia-scaffold module	Generate module files from a design config.
bactopia-scaffold subworkflow	Generate subworkflow files from a design config.
bactopia-scaffold test-data	Discover test data paths from existing module tests.
bactopia-scaffold tool	Generate all three tiers (module + subworkflow + workflow) for a bactopia-tool.

---

lookup

Look up package info from Anaconda and check for existing components.

bactopia-scaffold lookup PACKAGE [OPTIONS]

Arguments

Argument	Type	Required	Description
PACKAGE	STRING	Yes

Required Options

Option	Type	Default	Description
--bactopia-path	STRING		Directory where Bactopia repository is stored

Query Options

Option	Type	Default	Description
--channel	STRING		Force a specific channel (bioconda or conda-forge). Default: try bioconda first, then conda-forge
--max-retry	INT	3	Maximum times to attempt API queries. (Default: 3)

Output Options

Option	Type	Default	Description
--json	BOOL	false	Output flat JSON
--pretty	BOOL	false	Output pretty-printed JSON

Additional Options

Option	Type	Default	Description
--verbose	BOOL	false	Print debug related text
--silent	BOOL	false	Only critical errors will be printed

---

module

Generate module files from a design config.

bactopia-scaffold module [OPTIONS]

Options

Option	Type	Default	Description
--config	PATH		JSON design config file
--bactopia-path	STRING		Directory where Bactopia repository is stored
--dry-run	BOOL	false	Show what would be created without writing files
--json	BOOL	false	Output flat JSON
--pretty	BOOL	false	Output pretty-printed JSON
--verbose	BOOL	false	Print debug related text
--silent	BOOL	false	Only critical errors will be printed

---

subworkflow

Generate subworkflow files from a design config.

bactopia-scaffold subworkflow [OPTIONS]

Options

Option	Type	Default	Description
--config	PATH		JSON design config file
--bactopia-path	STRING		Directory where Bactopia repository is stored
--dry-run	BOOL	false	Show what would be created without writing files
--json	BOOL	false	Output flat JSON
--pretty	BOOL	false	Output pretty-printed JSON
--verbose	BOOL	false	Print debug related text
--silent	BOOL	false	Only critical errors will be printed

---

test-data

Discover test data paths from existing module tests.

bactopia-scaffold test-data [OPTIONS]

Required Options

Option	Type	Default	Description
--input-type	CHOICE (assembly, assembly_reads, genbank, gff, proteins, reads)		Input type to search for in existing tests
--bactopia-path	STRING		Directory where Bactopia repository is stored

Output Options

Option	Type	Default	Description
--json	BOOL	false	Output flat JSON
--pretty	BOOL	false	Output pretty-printed JSON

Additional Options

Option	Type	Default	Description
--verbose	BOOL	false	Print debug related text
--silent	BOOL	false	Only critical errors will be printed

---

tool

Generate all three tiers (module + subworkflow + workflow) for a bactopia-tool.

bactopia-scaffold tool [OPTIONS]

Options

Option	Type	Default	Description
--config	PATH		JSON design config file
--bactopia-path	STRING		Directory where Bactopia repository is stored
--dry-run	BOOL	false	Show what would be created without writing files
--json	BOOL	false	Output flat JSON
--pretty	BOOL	false	Output pretty-printed JSON
--verbose	BOOL	false	Print debug related text
--silent	BOOL	false	Only critical errors will be printed