Command line options¶
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
~/.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
--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 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
–create-report create the report directory –no-create-report opposite of –create-report -o,–html-report-directory ARG name of output directory