keeping intervals param deafult for all cases in GetPileupSummaries

[sk-sahu]

nf-core/sarek pull request

This PR address issue #299

if no interval is provided, all the variants will be used in the same interval param.

Based on, this doc -

Although the sites (-L) and variants (-V) resources will often be identical, this need not be the case.

If a subset of variants is being used then the interval bed file can come into the picture.

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[maxulysse]

@szilvajuhos What do you think of this suggestion?

[szilvajuhos]

My only issue is that we must test it before pulling it into dev. Or @sk-sahu have you tested already these?

[maxulysse]

I'm a bit concerned about using the germlineResource as a source for intervals when we have no intervals.
I'm thinking it might be safer to actually use the fasta source reference file (or something like the fasta.fai)