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:
- Add a new template directory below
cubi_tk/isa_tpl
. - Register it appending a
IsaTabTemplate
object to_TEMPLATES
incubi_tk.isa_tpl
. - 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.