Usage

How does the ZARP-cli work?

The zarp command accepts two kinds of arguments:

• Positional arguments: All positional arguments are interpreted as sample references, which can be paths to local RNA-Seq library files, paths to sample tables, or "run identifiers" assigned by either the Sequence Read Archive (SRA), the DNA Data Bank of Japan (DDBJ), or the European Nucleotide Archive (ENA). See below for a detailed description of the sample reference syntax.
• Command-line options: Optional arguments of the form --optional-arg, which either modify ZARP-cli's behavior or assign sample-, run- or user- specific metadata globally to all samples of a given ZARP-cli run. See below for a more detailed description of command-line options.

Sample references

The table below gives an overview of the supported basic sample reference types:

Type	Note	Examples
Path to local RNA-Seq library	Both absolute and relative paths are supported	/path/to/library_1.fq.gz, library_2.fq.gz
Path to local ZARP sample table	Both absolute and relative paths are supported	table:/path/to/sample/table_1.tsv, table:table_2.tsv
SRA/DDBJ/ENA identifier	Valid identifiers need to be matched by the following regular expression: (E|D|S)RR[0-9]{6,}	SRR123456, DRR7654321

The above basic types can further be amended by the following syntax fragments for further annotation:

Syntax	Description	Examples
PATH,PATH	Exactly two paths, separated by a comma and no white space, signify the two separate files for a paired-ended sequencing library; absolute and relative paths and mixes thereof are supported	/tmp/m1.fq.gz,/tmp/m2.fq.gz, mate_1.fq.gz,mate_2.fq.gz, mate_1.fq.gz,/tmp/m2.fq.gz
NAME@REF	A string separated from a non-table sample reference via the @ specifies a sample name (if not provided, a sanitized form of the base name of the file path is used)	se_sample@lib.fq.gz, pe_sample@m1.fq.gz,m2.fq.gz, remote_sample@ERR11223344

Different sample references can of course be mixed and matched to your heart's content!

Command-line options

Available command-line parameters are grouped into the following sections:

Section	Description
General	Next to sample references (the only required parameters!), these currently include the verbosity level and an option to provide a custom configuration file
Run modes	These parameters execute ZARP-cli in special modes, e.g., for initialization or to display the help screen
Sample-specific	These parameters modify globally set metadata for all samples of a run, unless overridden inside provided sample tables
Run-specific	These parameters modify the behavior of ZARP-cli or set metadata to describe runs
User-specific	These parameters will be included in the ZARP report, if available

A complete listing of all available CLI options can easily be printed to the screen, together with detailed descriptions, with the following command and will therefore not be repeated here:

zarp --help

Using the API

Next to using ZARP-cli's eponymous command-line interface, you can also integrate ZARP-cli's functionalities into your Python projects via its API.

The main entry point for ZARP-cli's high-level functionalities is the zarp.zarp.ZARP class.

A basic code snippet to trigger ZARP runs in your code might look like this:

from zarp.zarp import ZARP

# set up ZARP-cli configuration and attach sample references (not shown)

zarp = ZARP(config=config)
zarp.set_up_run()
samples = zarp.process_samples()
zarp.execute_run(samples=samples)

Configuring zarp.zarp.ZARP

To configure zarp.zarp.ZARP, have a look at the zarp.config.parser.ConfigParser class and the zarp.config.models.Config model.

A reference to the entire ZARP-cli API is provided in the API overview.