Nils Homer

The position of the variant is 1-based relative to the given contig, in this case transcript. So for a given transcript, you should have (from the GTF/elswhere) the strand of...

I’ll be honest that I have very little time for open source unpaid support given my work and family commitments. My apologies in advance, and feel free to reach out...

Can you justify why this is needed? We've been functioning for a while without it.

Moving to github actions in #76. Happy to see a new PR. Sorry for the long delay!

Alternatively, we could have `Assemble` create a lock file directly, which may be cleaner than having solve create the lock file and shoe horn it into the YAML.

I see [things like this](https://github.com/nf-core/rnaseq/blob/b89fac32650aacc86fcda9ee77e00612a1d77066/main.nf#L20C8-L31) in nf-core pipelines where params are overwritten (I think).

It would be great to have this be documented somewhere so we don’t have the rug pulled out from us for patterns that are in use today.

@tfenne I tried splitting all the changes I have made into discrete commits so you can review one-by-one, and then after each, I can rebase and fixup. The first one...

@tfenne I spent a bunch of time yesterday and today going over your comments. Highlights include: - attempted to document the main traits and classes - removed the `DependencyGraph` class...

Bump. Given a few more multi-sample pipelines and whole genome pipelines, this may be more relevant. @tfenne thoughts?