Support for both TCR and BCR

[leandrotiburske]

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[leandrotiburske]

Hi!

This PR aims to address support for both TCR and BCR (VDJ-T and VDJ-B) inputs, as discussed in issue #473.

To achieve this, I updated the feature_type enum and made the necessary modifications to the cellrangermulti module.

[fmalmeida]

Hi @leandrotiburske ;
I see that the PR contains a .diff for the cellranger/multi module.
Did you perform its modifications directly here in the scrnaseq repo or via the nf-core/modules repo?

[leandrotiburske]

Hi @fmalmeida ,

The modifications were performed directly here in the scrnaseq repo.

[fmalmeida]

Since cellranger/multi is a shared nf-core modules, we need first to update it upstream and then bring it to the repo.

More info here: https://nf-co.re/docs/contributing/contribute-components

[leandrotiburske]

Hi @fmalmeida,

I started working on updating the module upstream as you requested. While doing so, I noticed that after last week's merge, the Python template and main.nf appear to have diverged.

For example, the Python template contains:

#
# generate config file for cellranger multi
#
config_txt = (
    f"""${include_gex}
{gex_reference_path}
{frna_probeset}
${gex_options_filter_probes}

However, some of the variables (e.g., include_gex and gex_reference_path) that the template expects to receive from main.nf no longer seem to be defined there after the merge.

I also noticed that the template was last updated about 11 months ago, so I'm wondering whether the current mismatch is expected or if some changes may have been missed during previous updates.

Could you confirm whether this is a known issue? If so, would you prefer that I open an issue on nf-core/modules before proceeding with the upstream update?

Thanks!

[fmalmeida]

Hi @leandrotiburske ,
Is the current version you are seeing the same as the one after this PR here?

nf-core/modules#11066

If so, then indeed was a intended change where Mahesh helped migrating the inclusion checkers in order to fit better mutually exclusive files.

You can read more here:
#529

The scrnaseq pipeline would have to be slightly adapted to use the new version, but I can do that after you add the TCR and BCR support so the module update can be done only once to fix both issues.

If there are still mismatches like a variables that are not used anymore or scenarios that are not fully operational, please flag upstream as well.

So we can have the module fully operational upstream before we bring it in.

Does it make sense? Not sure if I actually answered or not, but feel free to ask for more clarification if needed.

:)