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### Description of the bug
I'm wondering if the `protocol` option is well interpreted for the adapter trimming.
If I use `--protocol illumina` or `--protocol qiaseq`, there is no difference in the…
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### Description of bug
This error occurs with the newest dev version ([8851655](https://github.com/MultiQC/MultiQC/commit/88516550ad52c07b5c9f12543c409fd54151f254) and before), potentially related …
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### Description of feature
The current CI includes many different parameters
- https://github.com/nf-core/rnaseq/blob/b89fac32650aacc86fcda9ee77e00612a1d77066/.github/workflows/ci.yml#L76-L90
- h…
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Hi @seandavi,
We're trying to run the pipeline on a mouse dataset, but we're running into the following error (I've only copied the tail end of it, since there's a lot of output, but I can share m…
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**Describe the bug**
Reads seem to not distribute uniformly across the genome. I expected some bias but there are long regions with coverage = 0 and others with coverage = 150, when the `neat read-si…
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Problem occured during migration from `nf-vallidation` to `nf-schema`. Aim is to migrate to newere sample sheet reader function.
Reproducible steps
1. Create new template pipeline
```
# nf-core…
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reported by @pcm32:
> Hi, we have someone trying to run cutadapt on a paired-end collection (a collection which elements are paired sequences). This was built from a Data Library using the List of …
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### Description of bug
nf-core/rnaseq passes *.duprateExpDensCurve_mqc.txt files to multiQC. The latest version (1.22.2) produces an error and traceback like the below.
Works fine in 1.21.
#…
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### Description of the bug
I was running some of the test datasets in preparation to input a high complexity dataset, and encountered an error with `PATHOGENSURVEILLANCE:ASSIGN_REFERENCES:SOURMASH_CO…
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