Add SVCallers: gridss and CNV: cnvkit,ascat

[dnousome]

Changes

Add SVCallers: gridss and CNV: cnvkit,ascat and SNV: deepsomatic
Additional bug fixes for strelka, varscan including for combining all somatic variants
Adds references for hg19/mm10

New callers specified using --svcallers ascat and --cnvcallers cnvkit

Issues

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• [ ] Write unit tests for any new features, bug fixes, or other code changes. testing framework not yet implemented
• Update docs if there are any API changes.
• If a new nextflow process is implemented, define the process container and stub.
• Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

[samarth8392]

ERROR ~ Error executing process > 'CNVhuman:freec_paired (1)'

Caused by:
  No such variable: GENOMEREF -- Check script '/data/CCBR/projects/techDev/LOGAN/./subworkflows/local/../../modules/local/freec.nf' at line: 45

Source block:
  """
  
  perl $FREECPAIR_SCRIPT \
      . \
      $FREECLENGTHS \
      $FREECCHROMS \
      ${tumor} \
      ${normal} \
      $FREECPILEUP \
      $GENOMEREF \
      $FREECSNPS \
      $CNVTARGETS

Issue

The GENOMEREF variable that was defined in copynumber.nf is missing from freec.nf