Add --skip_markduplicates

[maxulysse]

nf-core/sarek pull request

• add --skip_markduplicates cc @drpatelh @jfnavarro
• close Option to skip MarkDuplicates step #203

Just need to add some docs and sort out the mess I did, forgot to switch branches, so this one is base on my current PR regarding control-FREEC.
But as it's getting late, I'll finish tomorrow morning.

Many thanks for contributing to nf-core/sarek!

Please fill in the appropriate checklist below (delete whatever is not relevant).
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PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
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• CHANGELOG.md is updated
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[ggabernet]

It looks good to me!