Changes test data

[l-mansouri]

Overview

This PR aims to standardize the pipeline to better conform to the template, according to the jira ticket and the discussion on SLACK on how to handle mock data.

. There are workarounds for reference data when used in ci tests if reference data is too large for :github-actions: : https://github.com/lifebit-ai/finemapping/blob/dev/conf/data/data.config#L17 & https://github.com/lifebit-ai/finemapping/blob/dev/main.nf#L83 & https://github.com/lifebit-ai/finemapping/blob/dev/conf/tests/ci/test_ci_polyfun.config#L13

Purpose

This PR aims to standardize the pipeline to better conform to the template.

• 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

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

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

[monikrzyz]

Looks good to me!