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UPHL-BioNGS / Cecret

Reference-based consensus creation
MIT License
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WARN: Unable to fetch attribute for file... #114

Closed DrB-S closed 1 year ago

DrB-S commented 1 year ago

Are these warning messages a problem for the outgroup files or can I safely ignore them?

WARN: Unable to fetch attribute for file: /app/becksts/.nextflow/assets/UPHL-BioNGS/Cecret/configs/NC_063383.1.gff - Hash is inferred from Git repository commit Id WARN: Unable to fetch attribute for file: /app/becksts/.nextflow/assets/UPHL-BioNGS/Cecret/configs/NC_063383.1.gff - Hash is inferred from Git repository commit Id

erinyoung commented 1 year ago

🤦‍♀️

It means there's a typo in the path.

I've now fixed it.

erinyoung commented 1 year ago

You'll need to update your local version with

nextflow pull UPHL-BioNGS/Cecret
DrB-S commented 1 year ago

When I do that I get the following message: (base) [becksts@awsgenomep Cecret]$ nextflow pull UPHL-BioNGS/Cecret Checking UPHL-BioNGS/Cecret ... UPHL-BioNGS/Cecret contains uncommitted changes -- cannot pull from repository

erinyoung commented 1 year ago

That's a new error message.

What happens if you delete the associated nextflow asset?

DrB-S commented 1 year ago

I have been doing that. I just did that again and restarted, since I couldn't run "nextflow pull UPHL-BioNGS/Cecret" from the command-line.

erinyoung commented 1 year ago

Were you able to re-pull the repo with nextflow or are you still running into issues?

DrB-S commented 1 year ago

Doesn’t removing the Cecret folder from .nextflow/assets/UPHL-BioNGS do the same thing?

Stephen M. Beckstrom-Sternberg, PhD Bioinformatics Contractor

Arizona State Public Health Lab Arizona Department of Health Services Cell: (602) 653-5011 Email: @.***

On Aug 4, 2022, at 3:32 PM, Young @.***> wrote:

Were you able to re-pull the repo with nextflow or are you still running into issues?

— Reply to this email directly, view it on GitHub https://github.com/UPHL-BioNGS/Cecret/issues/114#issuecomment-1205833812, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVTVLJVKEIGZTZTS6AA4PU3VXRAHPANCNFSM55QI2YLQ. You are receiving this because you authored the thread.

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DrB-S commented 1 year ago

Yes. This issue is resolved.

erinyoung commented 1 year ago

Good! I was worried that more things were going wrong. Thank you for creating an issue!