Updates on the minimal settings

[maxulysse]

This one should be the last one on this series from me.
I also included some minor refactoring (sorry).

• Add a new step: prepare_recalibration

We're actually already saving the BAM and index files for the next step, but as recalibration can only happen with some know variants, there was actually no plan to restart from the calculation of these recalibration tables.
It is now possible.
The idea is to allow people to do preprocessing up until the preparation of the recalibration tables, and follow by some variant calling to allow a creation of know variants resource which can later be used to calculate and do the recalibration and then do some proper variant calling.
cf: https://gatkforums.broadinstitute.org/gatk/discussion/1247/what-should-i-use-as-known-variants-sites-for-running-tool-x

• fix --step recalibrate which had some issues.
• fix typo for output directory DuplicateMarked should have been DuplicatesMarked

nf-core/sarek pull request

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• This comment contains a description of changes (with reason)
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[maxulysse]

Just missing some docs