Matthias Zepper
Matthias Zepper
@sa501428 and others: Thanks for taking a look at it! Unfortunately, it escaped me that you were already working on refactoring the builds. In that case, you could still use...
Sadly, downloading exactly this pipeline version that contains the affected module will not be possible to support with the current nf-core download, [for reasons explained here](https://github.com/nf-core/tools/issues/2392#issuecomment-1682393518). Nextflow has received a...
This is no surprise. You need [to additionally specify another profile that will take care of all the dependencies](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline): `docker`, `singularity` or `conda` (not recommended, though).
That is not really what the `-resume` functionality is meant for. It enables fixing issues along the way that have caused a workflow execution to grind to a halt. It...
Since people complained about the poor performance, the generation of deduplication statistics if off by default now. You have to set the parameter `--umitools_dedup_stats` respectively `umitools_dedup_stats : true` in a...
Yes, you can increase the number of threads via a custom config. Please see the documentation on custom configs and [Tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources). I have some doubts, though, if the...
> I am assuming if I add more cpus, it will consider it as runThreadN value, right? Yes, because [the module is written in that way](https://github.com/nf-core/modules/blob/2be41ca2cc780eca4293d1b0dd3850b0b7ac40a3/modules/nf-core/star/align/main.nf#L55). You can also change...
Conversely, the strand-specific coverage information is what most people need, so I think there are good reasons to keep it like it is. Consider using the IGV functionality _Overlay Data...
I did manually test the change with the test profile and providing `extra_star_align_args = '--outFilterMultimapNmax 50'`, but it felt excessive to write a separate nf-test only for this one parameter...
Seems the tests are failing. Before I try to troubleshoot code in a language I do not know... do you, Jonathan, right away know where the problem is?