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Hello,
I believe there is a bug in the latest singularity recipe. While my experience with singularity is limited, I believe that in line 39 under %files, some files and directories are being attem…
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### Description of the bug
Error encountered when installing dev branch of fastquourum with latest nf-core/tools build.
@MatthiasZepper helped with a little digging.
>I think (but could not check b…
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### Version of Apptainer
What version of Apptainer (or Singularity) are you using? Run
`apptainer --version` (or `singularity --version`).
apptainer version 1.3.3-1.el8
### Expected behavi…
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We are using qsiprep on an HPC cluster that requires use of apptainer (i.e., singularity the next generation).
We found that when we run the singularity command as described [here](https://qsipre…
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### Cleanup
- [x] sylabs/singularity#2919
- [x] sylabs/singularity#2957
### Testing
- [ ] sylabs/singularity#2984
- [ ] sylabs/singularity#2989
- [x] sylabs/singularity#2990
- [ ] sylabs/…
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Hi,
I have installed DeconBenchmark in a conda environment on our HPC cluster. It has the singularity connection as I have checked with:
`babelwhale::test_singularity_installation(detailed = TRUE…
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I had trouble running a GUI over untrusted (`ssh -X`) X11 forwarding. The container was launched as a slurm job, which may interact with this. The container was launched with
```
singularity --sil…
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### Operating System
Ubuntu 22.04
### Other Linux
_No response_
### Workflow Version
wf-basecalling v1.4.2-g9c0f9db
### Workflow Execution
Command line (Local)
### Other workflow execution
_N…
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### Description of the bug
`rnaSPADES` step fails with the following error:
```
Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads)` terminated with an error exit status (12)
....…
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**Describe the bug**
When running a job on a system with Singularity, a user ran into an error during the SCE to h5ad conversion.
![image](https://github.com/user-attachments/assets/57e625b8-b6…