Improve documentation + code and update nf-core template and modules

[sci-kai]

This is the final PR for our first release to verison 1.0.0. It adds substantial changes to documentation, updates the nf-core template and modules and making the code more clear. Especially due to the nf-core template and module update the PR is quite huge. So I would kindly ask you to have a quick look into the imrpoved documentation and code improvements as mentioned below:

Documentation:

• Added detailed description of modules in README.md. Moved some description from docs/output.md here.
• Added pipeline tube plot as overview in README.md.
• Added step-by-step guide in docs/usage.md (without test sample for now).
• Added parameter documentation in docs/params.md using nf-core schema docs command.
• Reorganized output folder names and organization and updated docs/output.md accordingly
• Updated CHANGELOG.md and CITATIONS.md

Code improvements and bug fixes

• Reorganized configuration files in conf/ to have better overview.
• added some parameter checks in workflows/variantinterpretation.nf and give appropriate errors/warnings.
• added ensembl vep summary to multiQC output
• changed names of filtering module to make it more clear

nf-core updates

• Updated nf-core template to version 2.10.
• Added missing files shown from nf-core lint to be compliant with nf-core guidelines.
• Updated all nf-core modules. Also added ensembl-vep module as patched nf-core instead of local to receive updates.
• removed quay.io labels from local modules container definition (recommended for nf-core modules)

[feiloo]

This looks like a multiqc bug, but the "Variant Quality" diagram in the "multiqc_report.html is empty.

Also, everytime the plot is switched via the buttons like "Count SNP, COUNT Transitions, ..." a new unplot is empty and every click on the button creates a new html div element is created but never cleaned up.

[sci-kai]

Thanks for pointing that out. I could reproduce the Issue, but this is a general mutliQC problem that should not affect our release.