Template standardization

[l-mansouri]

Overview

This PR aims to standardize the pipeline to better conform to the template. DO NOT MIND the insane amount of COMMITS, there was an issue with the sync in my local repo! SORRY!

Purpose

This PR aims to standardize the pipeline to better conform to the template. It mainly involves:

• parametrisation of the container name, with the url of the container bein in conf/quay.config
• parametrisation of the paths of the reference data for the pipeline to better accommodate for different AWS regions using the params.reference_data_bucket parameter
• the collection of the reference/pipeline specific data in conf/data/data.conf
• implementation of extra config files as needed to better adhere to the guidelines

Acceptance Criteria/Jira Ticket

DEL-16132

Changes

• Refactors the container names
• Refactors nextflow.config accordingly
• Refactors conf/data/data.config to accommodate for the new parametrisation of the path
• Refactors the documentation to reflect changes
• Moved config file to better reflect the template
• Added some config file to better reflect the template

Internal CloudOS Tests

Not necessary if run in Internal CloudOS CI

• -profile test_full_family
• -profile test_full_multi_hpo
• -profile test_full_single_vcf

Client CloudOS Tests

• -profile <replace_with_profile1>
• -profile <replace_with_profile2>

PR Checklist

Author to check:

• The PR title is informative and begins with appropriate [Fix:|Feat:|Docs:] based on PR type
• This PR is raised to dev branch for DSL1 or DSL2-dev for DSL2 translations
• The description contains the acceptance criteria or link to the associated Jira ticket
• The description contains links to CloudOS tests covering all test cases in client environment

Reviewer to check:

• A new test profile covering new functions for acceptance criteria is created if it does not already exist
• Nextflow configs have associated profiles named to match the config basename
• The Jenkinsfile has been updated with current Nextflow profiles
• The internal_lifebit_cloudos_ci.yml has been updated to run all current Nextflow profiles
• Redundant tests have been removed
• The README.md has been updated with parameter changes and current results/ and conforms to the README.md guidelines
• The code is logical, readable, reasonably optimal and meets the acceptance criteria
• The containers folder has been updated with the necessary containers to run this pipeline if needed