Julianus Pfeuffer

### Description of feature For the release 1.0 we needed to move to a private server for CI since PRIDE was too unstable. We should move back at some point.

### Description of feature I am not sure but I think in some modules we could reduce the hardcoding of parameters in the script and pass them with "withName" "ext.args"...

### Description of feature We are ignoring the following nf-core standards: Please use the following naming schemes, to make it easy to understand what is going where. - initial process...

Add some CI checks for readthedocs branch

1

### Description of feature We removed the general CI jobs from the readthedocs branch. We should instead have different CI jobs like spellchecks and maybe sphinx generation.

### Description of feature From https://github.com/orgs/OpenMS/packages Image URL: ghcr.io/OpenMS/openms-executables:latest

### Description of feature As in proteomicslfq. Was not carried over.

Add more elaborate experimental design validation

2

### Description of feature After parsing the SDRF, we should check if the OpenMS experimental design is also up to the OpenMS standard.

### Description of feature Input check, pmultiqc and software version stuff should be universal for all (sub)workflows. So they all should be in the parent quantms workflow file

### Description of feature We have some smaller steps that take a very short time only. We could think about combining them, if we find that copying the data and...

### Description of feature In LFQ this is decided based on the peptide_quantification parameter: "shared_peptides" = greedy resolution ON "unique_peptides" = greedy resolution OFF