Add coverage cap param

[alkaZeltser]

Description

Closes #11

• Added parameter to collectHsMetrics controlling the coverage cap for coverage calculations
• Added default coverage cap parameter
• Added previously undefined default paramater for optional bait file path (empty string)

Testing Results

• Case 1: Default coverage cap with no user changes
  • sample: A-mini
  • input csv: /hot/user/nzeltser/pipeline-targeted-coverage/test/test.csv
  • config: /hot/software/pipeline/pipeline-targeted-coverage/Nextflow/development/unreleased/nzeltser-add-coverage-cap/default-coverage-cap/test.config
  • output: /hot/software/pipeline/pipeline-targeted-coverage/Nextflow/development/unreleased/nzeltser-add-coverage-cap/default-coverage-cap/targeted-coverage-nf-1.0.0-rc.1
• Case 2: User defined coverage cap
  • sample: A-mini
  • input csv: /hot/user/nzeltser/pipeline-targeted-coverage/test/test.csv
  • config: /hot/software/pipeline/pipeline-targeted-coverage/Nextflow/development/unreleased/nzeltser-add-coverage-cap/user-defined-coverage-cap/test.config
  • output: /hot/software/pipeline/pipeline-targeted-coverage/Nextflow/development/unreleased/nzeltser-add-coverage-cap/user-defined-coverage-cap/targeted-coverage-nf-1.0.0-rc.1

Checklist

• [x] I have read the code review guidelines and the code review best practice on GitHub check-list.

• [x] I have reviewed the Nextflow pipeline standards.

• [x] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• [x] I have set up or verified the branch protection rule following the github standards before opening this pull request.

• [x] I have added my name to the contributors listings in the manifest block in the nextflow.config as part of this pull request, am listed already, or do not wish to be listed. (This acknowledgement is optional.)

• [x] I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

• [ ] I have updated the version number in the metadata.yaml and manifest block of the nextflow.config file following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)

• [x] I have tested the pipeline on at least one A-mini sample.

[alkaZeltser]

One note: consider adding schema validation to validate params before a pipeline runs. Not necessary for this PR but maybe good to track as an open issue to add sometime in the future

What's that??

[yashpatel6]

Basically what's being implemented here using the module here