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### Operating System
Ubuntu 22.04
### Other Linux
_No response_
### Workflow Version
latest
### Workflow Execution
Command line (Local)
### Other workflow execution
_No response_
### EPI2ME …
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## Bug report
On HPC running nextflow with charliecloud.enabled=true submitting the pipeline call using bash -c 'nohup nextflow run ...'.
Observed error: `ch-run[xxxxx]: error: can't mkdir: : Fil…
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### Description of the bug
On my university's cluster, users are penalized (with priority reduction) for requesting more RAM than they actually use. So the fact that the pipeline requires at least 72…
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### Description of the bug
During full sized tests using aligner universc, the `UNIVERSC` process failed with "Essential container in task exited". Unfortunately the logs for the process are empty.
…
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Tasks that fail and are retried should have their intermediate files cleaned up for the failed attempt. Maybe as an opt-in behavior in case the user wants to debug
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@emilyncosta , your and @Ankita-1211 suggestions would be great regarding the `Readme` / `usage documentation`. Do you find it easy to understand and use?
Your needs would help @sharma-shruti and…
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Put publishDir directives in the nextflow.config file so they're more easily edited for runtime configuration.
See [how nf-core does it](https://github.com/nf-core/rnaseq/blob/master/conf/modules.c…
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## Bug report
When invoking nextflow via the CLI, some files can be specified as an S3 URL. Others cannot. This is not always clear from the documentation.
This may turn into a feature request, d…
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I am running the abinitio pipeline with :
params.yml :
```
subworkflow: 'abinitio_training'
genome: 'genome.fa'
maker_evidence_gff: 'maker_evidence.gff'
species_label: 'Lin_leo'
codon_table…
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Hello Isicle developers,
I try to reproduce the example of collision cross section. The Isicle was installed correctly according to the message
```
Requirement already satisfied: certifi>=2017.…