Describe the Question
Hi Eager Team, this isn't a bug so much as it is a question. I'm curious about why the qualimap and damageprofiler modules run on the output of samtools_filter rather than dedup? Perhaps it's a matter of personal preference, but I'd rather my coverage/depth estimates and allele frequency/substitution rates be calculated independent of PCR duplicates. For depth, it's to a
We should have something that documents on how to get a new pipeline properly released. The question pops up quite frequently and is something we could easily document using 2-3 screenshots, e.g. like this:
Custom configs are now hosted centrally at nf-core/configs. We need to think about where we host the documentation for running these config files. These are currently added on a per-pipeline basis but it would be good to also host them centrally so they are available to all pipelines.
This will also probably involve refactoring the current docs to deal with this.