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UPHL-BioNGS / Grandeur

UPHL's Reference Free Pipeline
GNU General Public License v3.0
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version.yml file in v4.0.20240214 #180

Closed whottel closed 5 months ago

whottel commented 6 months ago

Hello,

First of all thanks for all the improvements that you continue to make for grandeur. We were testing v4.0.20240214 (run with Nextflow v 23.10.1 ) and noticed some issues with the versions.yml that is getting created. When running the pipeline, I see this versions.yml is created in the grandeur directory. Capture1

Not sure if this is intended to still be here, or if a cleanup step is not working properly.

For other users at our lab the pipeline is failing due to this file and is causing a nextflow error:

error_log.txt

erinyoung commented 6 months ago

Oh no!

versions.yml is something that all nf-core workflows have. They don't seem to run into errors and I should dig deeper into why.

I should have this fixed by next week!

erinyoung commented 6 months ago

It looks like I need to add saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, to publishDir

erinyoung commented 5 months ago

@whottel , my apologies for taking so long with this!

This issue should now be resolved. Let me know if my assumption is incorrect!

whottel commented 5 months ago

No worries, thanks for the update! In initial tests it all seems to be working fine on our end.