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 prioriry.

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-dir ARG Reference search directories (replace in script) --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 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