Search test datasets
The nf-core test-datasets search subcommand provides functionality to interactively search existing test-datasets for pipelines and modules from the commandline.
Test-datasets are hosted on the on the nf-core/test-datasets github repository.
Not all files found on github can be searched with this subcommand.
Some auxiliary files like README, or LICENSE as well as all files starting with . are always ignored.
Search a branch for a data file
The subcommand fetches, filters and searches through the filetree of a branch of the test-dataset repository and prompts the user for a query, that can be tab-autocompleted. A query can be specified as a command line argument to pre-populate the search field and if the query is unambiguous return the matching file without prompting. A branch name to limit the search to is always required and if none is specified via the command line, the user will also be prompted to enter one.
To improve usability branch names can be entered via a tab-autocompletion. Alternatively, to list all branches see the list_branches subcommand.
Reusing the test-data files
As output from this subcommand, download links can be obtained or include statements for use in nf-core pipelines generated.
This uses the same flags -u/--generate-dl-url and -p/--generate-nf-path as the list subcommand.