fixes sample fastq output bug in cellranger mkfastq

[julicudini]

PR checklist

Closes #6189

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[atrigila]

Hi @julicudini , thank you for this PR. Some checks are not passing, but this is due to the nf-test snapshot of mkfastq not being updated. Could you run nf-core modules test --update? Thank you :)

[apeltzer]

Would also be good to output the Undetermined in a separate channel, similar to what bcl2fastq/bclconvert do at the moment - that way would behave more consistently :)

[nschcolnicov]

I was working on the PR for the same changes at the same time and missed the notifications on this one. I have already been testing the module on my PR with a new version of demultiplex that handles these changes, so it would make things simpler for me if we can merge this one https://github.com/nf-core/modules/pull/6194. And @julicudini you can address the changes for the other cellranger modules on this PR

[SPPearce]

@julicudini , are you still working on this?

[apeltzer]

I think this was fixed in https://github.com/nf-core/modules/pull/6194 already

[SPPearce]

I think this was fixed in #6194 already

I think the comment chain above is suggesting there are other modules that need adjusting in a similar manner, that weren't done in #6194.

[apeltzer]

Fair point, lets wait for @julicudini

[luisas]

@julicudini Is this PR still relevant?

We are doing some cleaning and trying to close PRs if they are not needed anymore :)

[apeltzer]

There was already an updated version of the cellranger module - maybe check if its fine there @julicudini and if not reopen? :-)