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nf-neuro

Test data infrastructure

Test data infrastructure

nf-neuro provides an infrastructure to host and distribute test data, freely available to all contributors. Access to this data is done through the dedicated subworkflow LOAD_TEST_DATA. Test data packages are listed in tests/config/test_data.json. Introspection of their content is available in VS Code only, using the Test Data Explorer extension. Once installed, it adds the Test Data Explorer to the explorer panel (Ctrl+Shift+E), which you can use to browse and download test data packages and their content.

To download test data inside your test workflows, first include the LOAD_TEST_DATA workflow in their main.nf :

include { LOAD_TEST_DATA } from '../../../../../subworkflows/nf-neuro/load_test_data/main'

The workflow has two inputs :

  • A channel containing a list of package names to download.

  • A name for the temporary directory where the data will be put.

To call it, use the following syntax :

archives = Channel.from( [ "<archive1>", "archive2", ... ] )
LOAD_TEST_DATA( archives, "<directory>" )

The archives contents are accessed using the output parameter of the workflow LOAD_TEST_DATA.out.test_data_directory. To create the test input from it for a given PROCESS to test use the .map operator :

input = LOAD_TEST_DATA.out.test_data_directory
  .map{ test_data_directory -> [
    [ id:'test', single_end:false ], // meta map
    file("${test_data_directory}/<file for input 1>"),
    file("${test_data_directory}/<file for input 2>"),
    ...
  ] }

Then feed it to it :

PROCESS( input )