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

The Cookiecutter directories are located in this module’s directory. Currently available templates are:

  • isatab-generic
  • isatab-germline
  • isatab-microarray
  • isatab-ms_meta_biocrates
  • isatab-single_cell_rnaseq
  • isatab-bulk_rnaseq
  • isatab-tumor_normal_dna
  • isatab-tumor_normal_triplets
  • isatab-stem_cell_core_bulk
  • isatab-stem_cell_core_sc

Adding Templates

Adding templates consists of the following steps:

  1. Add a new template directory below cubi_tk/isa_tpl.
  2. Register it appending a IsaTabTemplate object to _TEMPLATES in cubi_tk.isa_tpl.
  3. Add it to the list above in the docstring.

The easiest way to start out is to copy an existing cookiecutter template and registration.

More Information

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