nfcore template update with restructuring of workflow

[sci-kai]

This PR updates the nf-core template to the newest version 2.14.1. The new template includes major changes in the workflow structure. IMO those correspond to the changes suggested by @feiloo in our developer meeting to make the workflow more modular and compatible for combination (in that respect, sarek also adapts these changes in their dev branch). If you have any comments or additional changes, feel free to add them.

Summary of most important changes:

• restructuring of workflow: workflow/variantinterpretation.nf now only contains main workflow steps while Initialisation, validation and completion are separate subworkflows.
  • input channels are now defined in main.nf and not in the workflow/variantinterpretation.nf file
  • Pipeline initialisation and completion are now separate subworkflows called in main.nf workflow call. This removes the groovy scripts used in workflow/variantinterpretation.nf.
  • parameter validation is performed in PIPELINE_INITIALISATION subworkflow and is not anymore within workflows/variantinterpretation.nf.
  • new samplesheet check in PIPELINE_INITIALISATION subworkflow, removed previous samplesheet check via python script. I had to adapt the new samplesheet check to accept vcf files instead of fastq_1 and fastq_2 files.
• updates multiQC module from v1.17 to v1.21 and fixed errors coming with template changes in workflows/variantinterpretation.nf.
• added conda channels to nextflow.config

Additional changes by me (template-independent):

• fix of inconsistent default values in nextflow_schema.json
• named input channels supplied into the workflow VARIANTINTERPRETATION with "ch_" prefix to better distinguish from workflow-intrinsic channels and parameters.

[feiloo]

I now figured the assets paths to be a non issue. It occurred when my pipeline was erroneusly including the outermost CIOABCD_VARIANTINTERPRETATION workflow instead of VARIANTINTERPRETATION. It could still maybe be alleviated by using nextflows moduleDir instead of projectDir but isnt any problem atm this way.