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Currently, this pipeline will not run on the latest version of Nextflow. The error message " Nextflow DSL1 is no longer supported — Update your script to DSL2, or use Nextflow 22.10.x or earlier", app…
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## Bug report
### Expected behavior and actual behavior
When `cleanup = true` for a workflow that has specified a `bucket-dir` and has files that need to be cleaned up, the cleanup operation fa…
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### Description of the bug
Hello,
I am trying to run GSEA but I get an error when trying to process the GMT file I obtained from MSigDB.
Previously, I have executed the pipeline without the G…
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### Description of the bug
I ran the current version of pgsc_calc with 63 scorefiles on a single sample and got this error:
```
FATAL: container creation failed: mount /proc/self/fd/4->/usr/l…
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**Description**
I am encountering an issue with Bactopia versions 3.1.0 and 3.0.0 in my HPC environment. When submitting Bactopia jobs to the SLURM scheduler, the jobs consistently fail after around …
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Hi!
The docker image does not contain ps which makes it incompatible with nextflow runs which capture performance metrics for processes.
```
Command 'ps' required by nextflow to collect task …
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## Bug report
### Expected behavior and actual behavior
I should be able to use task in both the shell and stub sections, but if I do it generates a stack overflow error
### Steps to reproduce…
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**Is your feature request related to a problem? Please describe.**
Current documentation shows small examples. Working on real large datasets varies in some ways and has specific needs:
- limiting Da…
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## Bug report
When using the second preview version for publishing outputs from workflows the `output` block is required for files to be actually published. Nothing needs to be set within the bloc…
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Hi! I can't tell if there are any previous reports of this error, because I can't seem to see any other issues on the Github.
I recently ran a screen with the Zuber lab's 2-guide human library, usi…