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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
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`cpu` is no longer a variable in the SRA_Fetch task #362

Closed watronfire closed 4 months ago

watronfire commented 4 months ago

The most recent commit (0c011eda8911b7e8f034fe58c5762f9bf83f2722) broke the SRA_Fetch workflow because it removed the tilde and curly braces surrounding cpu.

https://github.com/theiagen/public_health_bioinformatics/blame/0c011eda8911b7e8f034fe58c5762f9bf83f2722/tasks/utilities/data_import/task_sra_fetch.wdl#L29

kapsakcj commented 4 months ago

Thank you for the heads up, we will get this fixed soon! For now I would recommend using the v1.3.0 release of the workflow to avoid this issue.

kapsakcj commented 4 months ago

I just made a quick code change to address this issue. You can also use the branch called cjk-sra-fetch-bugfix which was created off of the main branch just now so it's more up-to-date with the code on main

I'm testing in Terra now, but 99.99% confident it will resolve the error

watronfire commented 4 months ago

Awesome! Thanks for the quick response!

kapsakcj commented 4 months ago

@watronfire the bug has been resolved, the main branch for the SRA_fetch_PHB workflow is now functional again.

Thank you for reporting this bug! and thank you @sage-wright for the quick review 👍