Add HTML report

[sci-kai]

Add HTML report using datavzrd

This PR adds the generation of an HTML report based on the TSV file created by vembrane. This report will be the main output of the workflow and should help in interpreting the variants

Features

• New local module datavzrd.
• Generation of an excel file with datavzrd that can be accessed through the HTMl report.
• Splitting of the variant TSV file columns based on predefined groups using a python script preprocess_datavzrd.py. These generates separate tables, that are linked with each other in the HTML report and are separate separate tabs in the excel file.
• a datavzrd_config_template can automatically render tick plots, heatmaps and hyperlinks based on definitions in the annotation_colinfo.tsv file. The yaml file is rendered with the YTE engine and has access to the columns from the annotation_colinfo.tsv file. In general, this makes the adaptation, extension and design changes for the HTML report much more easy and adaptable through simple modifications of the annotation_colinfo.tsv file. Please have a look at the help text of the new parameters which describe these two new assets in detail.
• A draft for a HTML report design that is defined in the annotation_colinfo.tsv file. This should be discussed together and need to be extended and adapted based on design decisions.
• added an identifier for each variant that is based on the columns: "chrom","pos","ref","alt","id","Feature". The latter is added as the TSV file is per variant-transcript. This is used to reference between tables and define unique entries.
• new parameters:
  • report: boolean for generating report
  • datavzrd_config: optional, needs a template that is provided in assets/datavzrd_config_template.yaml
  • annotation_colinfo: optional, needs a annotation overview that is provided in assets/annotation_colinfo.tsv

To-Do's:

• It still needs to define docker and singularity containers with datavzrd and the necessary python packages for easy usage.
• refining the HTML report design: adding links, splitting and formatting columns as e.g. dbSNP entries, SIFT column, etc.

[sci-kai]

I fixed a bug with channel handling. Beforehand, it only generated one report for one sample, now the channels are combined so that each sample generates a report. I also changed the process resource requirements for vembrane table and datavzrd to more realistic requirements.