Felipe Marques de Almeida

Hi @rob-p, I am now trying to change the INDEX module. And I have a couple of questions: 1. I will not require "transcripts_fasta" anymore, right? Actually simpleaf will only...

Hi @grst and @rob-p, Now that we have `SIMPLEAF_INDEX` and `SIMPLEAF_QUANT` modules working, before going on ahead on implementation, I think is good to have a nice review and brainstorm...

Hi @rob-p, > About `txp2gene` What you said makes total sense. I will adjust to be in that way, to use the one from `simpleaf` but to expect a given...

Hi @rob-p , Just updated how `txp2gene` is handled base on your propositions. Please see whether you agree: 1. when indexing a built transcriptome with `--transcript_fasta` that is passed as...

Yes, I think this is where I stopped last time. It seems that the directory from simpleaf is not what alevinqc expects, or I did something wrong either in the...

Yes, I do think so. The modules are sticked to alevinqc version 1.10

So this is the problem. Because we are indeed using the [latest version available in bioconda](https://anaconda.org/bioconda/bioconductor-alevinqc), but it turns out that it is not up-to-date with the package.

Hi folks, I now need some help to properly reconfigure the workflow (or modules) so that the permitDir is generated by simpleaf and that the whitelist is properly used. This...

Hi @Khajidu , yes, they should be the same.

Now, to finalise this, we should address this: https://github.com/nf-core/scrnaseq/pull/139#issuecomment-1258005319 Anyone has an idea?