Matthias Zepper

> @MatthiasZepper I think the failure here is because the nf-test didn't run on the module PR (maybe touching the template file isn't enough), and we need to update the...

> For me this is good to go. I've given the MultiQC report a check, and it's looking good to me when I check for the recent issues. I did...

> could you check again? Pipeline run is queued and about to start as we speak (as I type). > Also, could you give me the UMI params you're testing...

> I've also looked into the UMI thing. I don't think it can ever have worked (unless there is some regression I was unaware of). I fear, I can't follow...

Hello Meng, Normally, you should be able to download the Singularity images together with the pipeline using `nf-core pipelines download -s "singularity"`. So there is not really a need for...

You may have seen that there [has been an update to nf-core pipelines download that now wraps nextflow inspect](https://nf-co.re/blog/2025/refurbushing-the-pipeline-download). [Please upgrade to tools 3.4.0](https://nf-co.re/blog/2025/tools-3_4_0#refactored-download-command). I hope this resolves your issues...

[This might](https://github.com/aws-samples/amazon-omics-tutorials/blob/main/utils/scripts/nf/__init__.py) serve as inspiration for some additional functionality if needed.

I just wanted to express explicit support for this proposal! While I am not familiar with the implementation details, I think, it is a very important fix. Transcriptomic alignments or...

Sorry for the late reply. Technically, this should already be the case. The code has a check that should prevent prompts from being shown in non-interactive sessions: https://github.com/nf-core/tools/blob/930ece572bf23b68c7a7c5259e918a878ba6499e/nf_core/download.py#L440-L444 Why this...

I presume, that the original poster does _not_ want to define a cache directory?