Felipe Marques de Almeida

General question, what's the plan for the implementation? `EMPTYDROPS_FILTER` should come right before matrices conversion and concatenation? Shall it be always on? Or have a `params.filter_emptydrops` parameter for it?

@nf-core-bot fix linting

The script expects a parameter called `--version` which is defined like this: ```python parser.add_argument( "-v", "--version", dest="version", default=3, help="Version for features file, defines expected file name (1=kallisto,=v3 cellranger).", ) ```...

Well, I agree that having it standard so they can used in the same way afterwards is a good idea. I gues, for example, instead of adding this `export` on...

Hi @lam-c , Thanks for opening the issue and making it so informative it *really* helps A LOT. Secondly, based on your second comment, I guess you already narrowed it...

Nice, so really is input source. Something similar must be happening in jbrowser. And the errors make sense because these days I changed the named output channels so I may...

Hi @lam-c , For the `REPORT` module, I think now I've fixed on your branch, which has the PR opened, the gff channel that is given as input. Maybe now...

Ok, Thanks. Although I fixed the input channel and is now passing the correct gff to it, there may be something wrong on the actual `.Rmd` file. I will check...

Hi @lam-c, When testing later today you remembered to pull the changes and use the latest version of your master branch? Then one that is bringing the changes to this...

Just saw! I now get it. The reports and modules are fine. The local copy of the report that goes on the `report_files` sub-directory, works fine. It has everything. >...