# Command line options

Running ngless –help will show you all the command line options. Here we describe the most important ones.

Most of the command line options can be set in a configuration file, which defaults to ~/.config/ngless.conf, but you can set this explicitly:

--config-file ARG
 Configuration files to parse

The [configuraton](configuration.html) section of the manual has more information on which options can be set in the configuration file. Whenever an option is set both in the config file and on the command line, then the command line will take priority.

Note that, like configuration files, _command line options **do not change the results**_. Any change in the results results from changing the NGLess script. Command line options change _how_ the results are computed, not what they should be.

## Using multiple threads

The main option is called -j and sets the number of threads.

-j,–jobs,–threads ARG Nr of threads to use

Using –strict-threads/–no-strict-threads controls whether this is a strict or soft upper limit.

--strict-threads
 strictly respect the –threads option (by default, NGLess will, occasionally, use more threads than specified)
--no-strict-threads
 opposite of –strict-threads

## Paths

NGLess can generate large temporary files. By default it uses the system’s temporary directory, but it is often a good idea to set it to a path with a lot of free disk space:

-t,–temporary-directory ARG
Directory where to store temporary files
--search-path ARG
 Reference search directories (replace <references> in script)
--index-path ARG
 Index path (directory where indices are stored)

## Debugging

A few options are useful for debugging:

-n,–validate-only Only validate input, do not run script –subsample Subsample mode: quickly test a pipeline by discarding

99% of the input
--trace Set highest verbosity mode
--no-trace opposite of –trace
--keep-temporary-files
 Whether to keep temporary files (default is delete them)
--no-keep-temporary-files
 opposite of –keep-temporary-files

## QC Reporting

--create-report
 create the report directory
--no-create-report
 opposite of –create-report
-o,–html-report-directory ARG
name of output directory

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