Sunbeam Commands

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] [--profile STR] 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).

Profile file options:

--profile: Name of the profile template to use (e.g. default, slurm) (default: default)

run

Executes the Sunbeam pipeline by calling Snakemake.

sunbeam run [-h] [-s PATH] [--target_list [TARGETS, ...]] -- <snakemake options>

Usage examples:

  1. To run all targets (not including extensions): sunbeam run --profile /path/to/project/

  2. To specify multiple targets: sunbeam run --profile /path/to/project/ --target_list all_decontam all_assembly all_annotation

-h/--help: Display help.
-s/--sunbeam_dir: Path to sunbeam installation.
--target_list: A list of targets to run successively.
<snakemake options>: You can pass further arguments to Snakemake after ``--``, e.g: ``$ sunbeam run -- --cores 12``. See http://snakemake.readthedocs.io for more information.

Tip

The --profile option is a snakemake option but should be used whenever using sunbeam run. The main sunbeam snakefile requires a config object to be defined and the profile created by sunbeam init will always specify a config file to get that from.

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:

  1. To update a config file in place:

    sunbeam config update -i my_config.yml

  2. 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:

  1. To apply a set of defaults to an existing config file in place:

    sunbeam config modify -i -f defaults.yml my_config.yml

  2. 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. 'qc: {minlen: 48}').
-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.

extend

Install the extension at the given URL.

sunbeam extend [-h] [-s PATH] github_url

-h/--help: Display help.
-s/--sunbeam_dir: Path to sunbeam installation.