Update documentation

[kubranarci]

Is your feature request related to a problem? Please describe

VEP annotation description is missing in README

Describe the solution you'd like

VEP annotation description is missing in README

Describe alternatives you've considered

No response

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[kubranarci]

also fix --download parameter in ENSEMBL_VEP

fix annotated_vcf = ENSEMBLVEP_VEP.out.vcf.map{ it -> tuple( it[0], it[1])}

[kubranarci]

remove vep_out_format

[kubranarci]

remove vep_include_fasta

[kubranarci]

remove species

[kubranarci]

remove vep_version

[kubranarci]

can I use
vep_cache = 's3://annotation-cache/vep_cache/'

[kubranarci]

fix this:
We thank the following people for their extensive assistance in the development of this pipeline:

TODO

Nagarajan Paramasivam @NagaComBio [email protected]

[kubranarci]

add vep params:

"vep_params": {
  "title": "Annovar options",
  "type": "object",
  "description": "Options for Annovar",
  "default": "",
  "properties": {
    "vep_cache_version": {
      "type": "string",
      "default": "110",
      "fa_icon": "fas fa-vep",
      "description": "VEP Cache version"
    },
    "vep_genome": {
      "type": "string",
      "default": "GRCh38",
      "fa_icon": "fas fa-vep",
      "description": "VEP genome"
    },
    "vep_cache": {
      "format": "file-path",
      "mimetype": "text/plain",
      "default": "null",
      "fa_icon": "fas fa-vep",
      "description": "File path to the VEP cache"
    },
    "download_cache": {
      "type": "boolean",
      "default": "false",
      "fa_icon": "fas fa-vep",
      "description": "Turn it on to download cache file"
    },
    "outdir_cache": {
      "type": "string",
      "default": "null",
      "fa_icon": "fas fa-annovar",
      "description": "Cache file directory to save, if download_cache is true"
    }
  }
},