[FEATURE] Update BAMTOFASTQ10X for multiplexed samples

[herpov]

Is your feature request related to a problem? Please describe

The current implementation of BAMTOFASTQ10X converts .bam files til .fastq files and locates the outputs in the working directory. The process emits all files with the .fastq.gz extension.

However, files are actually located in a nested directory. The top level directory can be named by giving a prefix as input to the tool. The next level may contain one or more directories depending on whether the given .bam file consisted of multiplexed samples. In these subdirectories we may find GEX and CMO .fastq.qz files, respectively.

Describe the solution you'd like

I'd like the BAMTOFASTQ10X process to expect a nested output, and emit all .fastq.gz files. The top level directory should be named with the meta.id of the input .bam file.

Describe alternatives you've considered

No response

Additional context

This update is relevant to a PR for the nf-core/scrnaseq pipeline: PR