tiny bug in theiavalidate export_two_tsvs task - Githubissues

theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.

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tiny bug in theiavalidate export_two_tsvs task #360

Closed kapsakcj closed 7 months ago

kapsakcj commented 7 months ago

:bug:

:pencil: Describe the Issue

The wc commands in the export_two_tsvs task do not work. It doesn't cause a workflow failure, but the command seems fail.

This line specifically: https://github.com/theiagen/public_health_bioinformatics/blob/0015440e5e25f9432d64c1e562cce633e2427de5/tasks/utilities/task_validate.wdl#L36

Error message seen in workflow logs:

wc: AR_isolate_panel_sample: No such file or directory
wc: ClearLabs_sample: No such file or directory

because the TSV file is not found. Likely just need to add a file suffix? (not sure if path needs altering too or not, need to check)

:repeat: How to Reproduce

Was this run on the Terra platform?
- Terra on GCP or Azure?
Or were the workflows run locally using miniwdl or cromwell?
- What was the exact command was used to launch the workflow?
If possible, we may ask you to share your Terra workspace with us. Usually READER access is sufficient, but we may ask for WRITER access if we need to make changes to the workspace to reproduce the issue.

:fishing_pole_and_fish: Expected Behavior

:floppy_disk: Version Information

:information_source: Additional Information