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### Have you checked the docs?
- [X] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [X] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules)
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Dear 10X team,
I was wondering whether it would even be legal to include `loupeR` into a Docker container to run a Nextflow pipeline and output the Cloupe file (from a Seurat object, so the cloupe fi…
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[//]: # (Please do not include your AWS account or credentials as part of the bug request.)
**Describe the Bug**
`agc workflow run` will zip whatever is at the `sourceURL` of the workflow in qu…
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The underlying processx (nextflow) has to keep running after closing the browser window. When it finishes, notify user (pass email as an input in shiny?).
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## Bug report
### Expected behavior and actual behavior
Running an nf-core pipeline would download the charliecloud images on-demand.
When multiple different processes are scheduled at the s…
fa2k updated
8 months ago
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### BioProject Checklist:
---------------
- [x] PRJNA524691
- [x] PRJNA513863
- [x] PRJNA488534
- [x] PRJNA309491
Follow the [Gene Expression Protocols](https://github.com/mestato/stat…
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The following is courtesy @heuermh
> In nf-core, it is a best-practice (and generated by the nf-core getting-started template) to capture software versions
>
> https://github.com/nf-core/rnaseq/…
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I noticed that the workflow expects the existence of a `[default]` user profile in `.aws/credentials` and `.aws/config`, and that that user be the one with access to the aws batch serializer. I did no…
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Nextflow should automatically trim any trailing whitespace from a parsed `container` directive before attempting to pull it.
For example: https://github.com/nf-core/modules/blob/f9c512bea532dbe9c043c…
ewels updated
3 months ago
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### Ask away!
ERROR ~ Error executing process > 'POREC:merge_pairs (1)'
Caused by:
Process `POREC:merge_pairs (1)` terminated with an error exit status (1)
Command executed:
# pass a qu…