Plugin updates and resource optimization

[nakib103]

Related to ENSVAR-6218

• Updates to VEP config ini file
  • Added following plugins -
    • REVEL
    • ClinPred
    • Downstream
    • Add pCADD
  • Allow some plugin files to be absent (just skip) , e.g - MaveDB and AlphaMissense do not have file for GRCh37 assembly.
  • Update gnomAD v4.1 file locations and add gnomAD frequency for all HPRC assemblies
• Resource optimisation -
  • Memory -
    • Added low, medium, and high type resource. And removed separate human profile.
    • Added RunVEP memory that depends on bin size.
    • Separate wigToBigWig process as it takes more memory and added memory based on wig file size.
    • Added remove_variants and summary_stats memory based in vcf file size.
    • Added split_vcf memory as fixed 32GB (probably can be more refined later)
  • Storage -
    • Summary stats was taking a lot of storage as it work on uncompress file. Made it so that it can work on compress file and take less storage.
• Accustom nextflow-vep changes -
  • Update run_vep sub_workflow arguments, related to change in this PR - Nextflow: Accept and split non-VCF input formats ensembl-vep#1675
  • Update the expected output filename from nextflow-vep (used as tag in run_vep sub_workflow), related to change in this PR - https://github.com/Ensembl/ensembl-vep/pull/1675/files#diff-b40e82cf98d3bf8cb166f5ef961695009b72591d9800fa738d8aad7752db5914R35
• Allow force creation of cache and FASTA for human too. Updated to download FASTA and cache for human 37 assembly.
• Bugfix: skip plugin if file does not exist. Adding skip option to check_plugin_files function was adding plugin even if file not present instead of skipping. Fixed that bug. This bug was causing several folds slowness due to Conservation plugin with wrong file.
• Bugfix: pipeline failed if source had / in its name. Replacing it with ASCII value.
• Print pipeline summaries and generate reports by default.