Sunbeam Commands¶
Contents
sunbeam [-h | -v] <subcommand>
-h/--help: Display help.
-v/--version: Display version.
Tip
This is the version given by semantic_version in sunbeamlib. For commits
and branches this may differ from the version given by git that is used
for things like environment naming.
init¶
Initialize a new Sunbeam project in a given directory, creating a new config file and (optionally) a sample list.
sunbeam init [-h] [-f] [--output FILE] [--defaults FILE] [--template FILE] [--data_fp PATH] [--format STR] [--single_end] project_fp
-h/--help: Display help.
-f/--force: Overwrite files if they already exist.
--output: Name of config file (default: sunbeam_config.yml).
Config file options:
--defaults: Set of default values to use to populate config file.
--template: Custom config file template, in YAML format.
Sample list options:
--data_fp: Path to folder containing ``.fastq.gz`` files.
--format: Filename format for --data_fp (default: guessed).
--single_end: Fastq files are in single-end, not paired-end, format for --data_fp.
project_fp: Project directory (will be created if it does not exist).
run¶
Executes the Sunbeam pipeline by calling Snakemake.
sunbeam run [-h] [-s PATH] -- <snakemake options>
-h/--help: Display help.
-s/--sunbeam_dir: Path to sunbeam installation.
<snakemake options>: You can pass further arguments to Snakemake after ``--``, e.g: ``$ sunbeam run -- --cores 12``. See http://snakemake.readthedocs.io for more information.
config¶
sunbeam config [-h] {update,modify} ...
-h/--help: Display help.
update¶
Updates a config file to be compatible with the active version of sunbeam.
sunbeam config update [-h] [-t FILE] [--strict] [-i | -o FILE] config_file
Usage examples:
- To update a config file in place:
sunbeam config update -i my_config.yml
- To write an update copy to a new file:
sunbeam config update old_config.yml -o new_config.yml
-h/--help: Display help.
-t/--template: Path to custom config file template, in YAML format.
--strict: Remove keys that no longer exist in the new config file.
-i/--in_place: Alters config file in place.
-o/--out: Where to write modified config file.
config_file: Existing config file to update.
modify¶
Modifies a config file with the specified changes.
sunbeam config modify [-h] [-s STR | -f FILE] [-i | -o FILE] config_file
Usage examples:
- To apply a set of defaults to an existing config file in place:
sunbeam config modify -i -f defaults.yml my_config.yml
- To change a single key:value pair in the ‘mapping’ section:
sunbeam config modify -i -s 'mapping: {keep_unaligned: True}'
-h: Display help.
-s/--str: YAML string (e.g. 'blast: {threads: 4}').
-f/--file: YAML file with new config values.
-i/--in_place: Alters config file in place.
-o/-out: Where to write modified config file.
config_file: Existing config file to modify.
list_samples¶
List the samples found in the specified directory.
sunbeam list_samples [-h] [-s] [-f STR] data_fp
-h/---help: Display help.
-s/--single_end: Samples are single-end (not paired-end).
-f/--format: Filename format (e.g. {sample}_R{rp}.fastq.gz) (default: guessed).
data_fp: Path to folder containing reads.