[FEATURE] Return primary alignment bam file and index in nf-core/fastq_align_bamcmp_bwa subworkflow

[paddyharker1005]

Is your feature request related to a problem? Please describe

Following on from issue #5564 which was addressed by #5565 where the alignment stats of the primary alignment are now returned by the subworkflow. If you are interested in unmapped reads (e.g for metagenomic analysis), these cannot currently be used if using bamcmp, as bamcmp does not return the original unmapped reads from the primary alignment in the resulting bam file.

Describe the solution you'd like

It would be good if the fastq_align_bamcmp_bwa subworkflow returned the primary alignment bam file and index so that the unmapped reads can be used.

Describe alternatives you've considered

No response

Additional context

No response