Matthias Zepper

While backporting the config changes to `rnaseq 3.8.1` (_since we run the old pipeline version with the latest MultiQC_), Anand had to introduce those changes to make the custom content...

This does not really have anything to do with `nf-core download`. Whether you pre-download the pipeline or directly reference the GitHub repo: If you run a particular revision of a...

> For some reason I misinterpreted the line "a significant rewrite for the nf-core download infra" to refer to how the modules use singularity/apptainer to pull containers On a second...

Frankly...no 😆. With not _hard coded with singularity_ I actually also meant _additionally hard coded with apptainer as well_. Since I am not involved in the modules, DSL and linting...

Some progress: - Vlad Savelyev speedily fixed the ["_Multi Module Multi QC issue_"]( https://github.com/MultiQC/MultiQC/issues/2584) for us, and the MultiQC release 1.22.2 was pushed just for us. Patching the MultiQC module...

> OK, I know the fix @MatthiasZepper, I sorted this in riboseq. The issue is that the file structure is flat by the time it gets to MultiQC. > So...

Thank you so much! I will try my best to finish this quickly now! > though I note that the trimgalore subworkflow doesn't do a post-trim FASTQ, which we might...

I think/hope/wish I am done with this PR. It now fixes 3 out of the 4 issues that were spotted with the _TrimGalore! renaming_ being left. However, I perceive this...

> Great, thanks @MatthiasZepper ! Just to be clear, you don't need an updated MultiQC? It did need changes to MultiQC, since the previous version was not working. However, the...

> Hope you don't mind @MatthiasZepper - just illustrating in those last couple of commits what I meant. So use the module in its updated form, but also have a...