[FEATURE] make picard markduplicates smarter

Is your feature request related to a problem? Please describe

picard markduplicates does not follow current best practices with regard to duplicate type tagging, UMI usage, and "free" index creation

Describe the solution you'd like

I'll add some logic to the module to detect presence of RX tags, auto-create an index (which you get for free with --WRITE_INDEX), and illumina instrument type detection.

Describe alternatives you've considered

I was worried that
according to https://nf-co.re/developers/modules#inputoutput-options
such smarts should not be added but after a bit of conversation in slack, it seems a PR might be welcome.

some "pros" to having this logic:

• encourages scientific best practices
• bams 'in the wild" will be more accurate
• very low risk of doing something wrong

some "cons"

• more responsibility to keep up with best practice (not sure this is really a con... seems like a responsibility for a workflow maintainer anyway)

Are there other cons that I'm not considering?

Additional context

No response

Start at the Picard MarkDuplicates module and review how duplicate type tagging, RX tags, --WRITE_INDEX, and Illumina instrument detection are currently handled. Define the expected behavior for each case, then add focused tests showing that the module applies the requested best-practice logic without breaking existing options.