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unrelated wf testing update
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hexylena committed May 16, 2023
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Expand Up @@ -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.

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