[FEATURE] cellrangerarc/count should allow multiple input files with the same basename

Is your feature request related to a problem? Please describe

E.g., a user may run ATAC and GEX on the same sample but put output in different folders, naturally resulting in a structure like atac_folder/sampleA_S1_L001_R1.fastq.gz and gex_folder/sampleA_S1_L001_R1.fastq.gz. This would work in native cellranger arc, but it breaks the module with a filename collision error.

Describe the solution you'd like

To provide the same features as the underlying tool and accommodate this intuitive file naming scheme, the module should account for this possible structure.

Describe alternatives you've considered

Force users to rename files or rename them upstream. Neither seem like good, maintainable practice.

Additional context

No response