Hi All, I was looking at the input file structure required by the pipeline, and I noticed that it starts from the folder where the FASTQ files are placed, rather than from a list of FASTQ files as in nfcore/single-cell pipelines. Do you plan to implement this feature in the future to allow direct reading of FASTQ files?

Hi, Sara! That might be workable, I'd have to think about it a bit more (we have some pipeline logic related to

tar.gz

files that would be affected). Any particular reason why you'd want it done like that, other than it's usually how it's done in nf-core pipelines? This is relevant since Space Ranger itself only handles a directory, rather than the FASTQ files themselves (which is opposite how it is commonly done for many other tools).

Hi Erik! To better fit the pipeline with the ones we already use at our facility. Anyway, if it helps, we can take care of the implementation ourselves. :)

We're of course always open to PRs! Might not happen much now over summer from our end

I noticed that there's a

visium-hd

branch currently in development. I was wondering if the

dev

branch can still be used for Visium HD analysis, or if it's necessary to use the specific

visium-hd

branch?

No,

dev

can't be used for Visium HD data, but the

visium-hd

branch is pretty mature and will be merged soon (I hope), so you can probably just use that branch