added folder structure for usage tutorial

[lescai]

In order to display correctly a nested structure in the usage page for Sarek, we modify the pipelines.json as

"doc_files": [
                        "docs/output.md",
                        "docs/usage.md",
                        "docs/usage/variantcalling/introduction.md",
                        "docs/usage/variantcalling/theory.md",
                        "docs/usage/variantcalling/sarek.md",
                        "docs/usage/variantcalling/interpretation.md"
                    ],

this will add one subfolder to /usage and the tutorial pages under the topic, thus allowing additional tutorials for different topics to be added in the near future.

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[mashehu]

no need to do this. if you have it in the sarek dev branch, it will update the pipelines.json