MarkDuplicates Input specificity and input refactor.

[johnoooh]

When using MarkDuplicates on an HPC with scratch enabled, the globbed *.bam copys both the input and output bam from scratch to the work directory. The output needed to be more specific. It is now ${prefix}.bam for the output so it now targets the output bam/cram instead of all files with the right file extension. For more details see the issue.

This should fix the issue for MarkDuplicates but be on the lookout for other modules where this occurs.

The second part of this may be more controversial but I found the bam/cram declaration to be a bit difficult to read. Prefix did not actually mean prefix here, it meant ${prefix}.bam. Because of this it required some logic later on to change this to cram. I cleared this up and hopefully made it easier to read.

PR checklist

Addresses ##7792, but more modules could have issues.

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[SPPearce]

I think there is another open PR to pipe the cram output straight from mark duplicates too.