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 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


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
--index-path ARG         Index path (directory where indices are stored)


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
                         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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