diff --git a/faqs/gtn/gtn_workflow_testing.md b/faqs/gtn/gtn_workflow_testing.md index 8976d53ee225b..716b2317fe9b3 100644 --- a/faqs/gtn/gtn_workflow_testing.md +++ b/faqs/gtn/gtn_workflow_testing.md @@ -54,13 +54,38 @@ contributors: [hexylena] 10. If the files in test-data are already uploaded to Zenodo, to save disk space, you should delete them from the `test-data` dir and use their URL in the `-tests.yml` file, as in this example: - ``` - - doc: Test the M. Tuberculosis Variant Analysis workflow - job: - 'Read 1': - location: https://zenodo.org/record/3960260/files/004-2_1.fastq.gz - class: File - filetype: fastqsanger.gz - ``` - -11. Contribute all of those files to the GTN in a PR. + ```yaml + - doc: Test the M. Tuberculosis Variant Analysis workflow + job: + 'Read 1': + location: https://zenodo.org/record/3960260/files/004-2_1.fastq.gz + class: File + filetype: fastqsanger.gz + ``` + +11. Add tests on the outputs! Check the [planemo reference if you need more detail](https://planemo.readthedocs.io/en/latest/test_format.html). + + ```yaml + - doc: Test the M. Tuberculosis Variant Analysis workflow + job: + # Simple explicit Inputs + 'Read 1': + location: https://zenodo.org/record/3960260/files/004-2_1.fastq.gz + class: File + filetype: fastqsanger.gz + outputs: + jbrowse_html: + asserts: + has_text: + text: "JBrowseDefaultMainPage" + snippy_fasta: + asserts: + has_line: + line: '>Wildtype Staphylococcus aureus strain WT.' + snippy_tabular: + asserts: + has_n_columns: + n: 2 + ``` + +12. Contribute all of those files to the GTN in a PR.