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Update scripts and NextFlow flows#10

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chdominguez wants to merge 1 commit intoValldHebron-Bioinformatics:mainfrom
NBDsoftware:genotyping_references_fixes
Open

Update scripts and NextFlow flows#10
chdominguez wants to merge 1 commit intoValldHebron-Bioinformatics:mainfrom
NBDsoftware:genotyping_references_fixes

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@chdominguez
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This PR includes the changes present in SEVENTEROVIR. Please take a look at the changes before mergin them because there are some things which I think are not needed, specifically this part:

fstStep.view()
scdStep.view()
inputs.view()

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