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## Bug report
### Expected behavior and actual behavior
I expected module binaries under `projectDir/resources/usr/bin` to be usable in `projectDir/main.nf` but they arent found.
It is possibl…
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### Description of the bug
Hello,
a samples.csv that was working in 3.15.1 is not accepted anymore.
The file has numeric sample ids. Prepending them with x makes it work again.
However numeric sample…
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## Bug report
### Expected behavior and actual behavior
I mention both `pull` and `run` because that is how I found the bug, but I confirmed it with just `pull`.
Expected:
Calling `nextflo…
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### Description of the bug
Hi,
Thank you very much for developing this amazing tool.
I was trying to use funcscan on my FASTA dataset, but I encountered issues with automatically downloading the da…
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## Bug report
If I use a cloudcache, Nextflow clean does not work.
### Expected behavior and actual behavior
Nextflow should be able to use the cloudcache and clean up the working dir, howev…
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### Description of the bug
Hey, on the current version 3.17.0, I get:
`Error in findColumnWithAllEntries(ids, metadata) : No column contains all vector entries`
from:
```
Error executing proc…
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I am having issues as I can't run Docker on my laptop and our big processing machine is running Windows Server (it's a VM) which won't run Docker without $$$. Is there a way to get into Nextflow or so…
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For our specific project at the lab we implemented exomiser into a nextflow workflow along with others. Its time now to elevate exomiser to its own workflow and publish it on nf-core if possible. Plea…
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## Fail tasks where stageOut fails
This is similar to existing issue https://github.com/nextflow-io/nextflow/issues/3372, but instead of being concerned with the `publishDir` step (run work directo…
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### Description of the bug
Dear community.
I am having problems running the GTDBTK step in the mag pipeline, this is what I got as an error:
![Image](https://github.com/user-attachments/assets/d00a8…