✨ deal with CRAM alignments

[bunop]

This PR will enable CRAM alignment and will close some issues which aren't required anymore: RG will be added in the alignment step and indexing will be performed with the nf-core workflow.

• closes ✨ deal with CRAM aligments #9
• closes ⚡ Add RG in alignment step #57
• closes 🔥 can samtools/index be removed #56

[github-actions]

nf-core lint overall result: Passed ✅

Posted for pipeline commit 2567919

+| ✅  18 tests passed       |+
#| ❔  25 tests were ignored |#

❔ Tests ignored:

• files_exist - files_exist
• nextflow_config - nextflow_config
• files_unchanged - File does not exist: CODE_OF_CONDUCT.md
• files_unchanged - File does not exist: .github/.dockstore.yml
• files_unchanged - File does not exist: .github/CONTRIBUTING.md
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/feature_request.yml
• files_unchanged - File does not exist: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File does not exist: .github/workflows/branch.yml
• files_unchanged - File does not exist: assets/email_template.html
• files_unchanged - File does not exist: assets/email_template.txt
• files_unchanged - File does not exist: assets/sendmail_template.txt
• files_unchanged - File does not exist: assets/nf-core-nf-resequencing-mem_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-nf-resequencing-mem_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-nf-resequencing-mem_logo_dark.png
• files_unchanged - File does not exist: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
• actions_ci - actions_ci
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/nf-resequencing-mem/nf-resequencing-mem/.github/workflows/awstest.yml
• actions_awsfulltest - actions_awsfulltest
• pipeline_todos - pipeline_todos
• pipeline_name_conventions - pipeline_name_conventions
• merge_markers - merge_markers
• multiqc_config - multiqc_config

✅ Tests passed:

• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - LICENSE matches the template
• files_unchanged - .github/workflows/linting_comment.yml matches the template
• files_unchanged - .github/workflows/linting.yml matches the template
• readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
• readme - README Zenodo placeholder was replaced with DOI.
• template_strings - Did not find any Jinja template strings (166 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• modules_json - Only installed modules found in modules.json
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

• nf-core/tools version 2.13.1
• Run at 2024-03-27 10:18:57