Manual for isa-tpl

cubi-tk isa-tpl: create ISA-tab directories using Cookiecutter.

You can use this command to quickly bootstrap an ISA-tab investigation. The functionality is built on Cookiecutter.

To create a directory with ISA-tab files, run:

$ cubi-tk isa-tpl <template name> <output directory>

This will prompt a number of questions interactively on the command line to collect information about the files that are going to be created. The requested information will depend on the chosen ISA-tab template. It is also possible to pass this information non-interactively together with other command line arguments (see cubi-tk isa-tpl <template name> --help).

The completed information will then be used to create a directory with ISA-tab files. It will be necessary to edit and extend the automatically generated files, e.g. to add additional rows to the assays.

Available Templates

These have been moved to a separate repository: see cubi-isa-templates.

Adding Templates

See cubi-isa-templates.

More Information

Also see cubi-tk isa-tpl CLI documentation and cubi-tk isa-tab --help for more information.