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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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Change relative paths to absolute paths in .dockstore.yml #346

Closed kathy-t closed 4 months ago

kathy-t commented 4 months ago

Hello,

I am a software developer at Dockstore. This PR addresses the issue in https://github.com/dockstore/dockstore/issues/5806 that was reported by @cimendes.

Prior to Dockstore's 1.15 release, relative paths were being inconsistently and unreliably processed in various parts of our system. Therefore, in this release, we have more explicitly deprecated the use of relative file paths in our .dockstore.yml so all workflows with relative paths are now considered as invalid. This change has impacted your workflows because your test parameter file paths are relative which is invalid and prevents Dockstore from updating your workflows.

Thus, I have created this PR to change the relative file paths to absolute paths so that your workflows are considered valid again in this new release.

Thank you! Kathy - Dockstore

kapsakcj commented 4 months ago

Thanks Kathy, appreciate the PR and information! I just made PR #347 and we may end up going with that instead just to keep things organized how we prefer.

kapsakcj commented 4 months ago

@kathy-t We appreciate the speedy response and help here. We were quite worried when we discovered this, but this is an easy fix!