feat: CLIN-3090 Save logs and move initialization logic to PIPELINE_INITIALISATION

[LysianeBouchard]

Warning: THIS IS A DRAFT, NOT READY FOR REVIEW THIS PR IS TOO BIG, I WILL SPLIT IT.

Changes:

• Modified PIPELINE_COMPLETION workflow to save nextflow log file in specified output directly
• Move initialization logic from PostProcessing workflow to PIPELINE_INITIALISATION workflow
• Fix issues with test sample sheet:
  • urls not found for gvcf files
  • wrong column name
  • one line per family instead one line per sample

Note: The copied log file is not entirely complete. It will miss a few logs from the completion handler and other Nextflow internal handlers (e.g., reports). However, the missing logs should not contain any critical information for debugging.

Tests description

I run the linter and double check that there is no new warning in comparison to the main branch. Actually we have 39 warnings instead of 41 because. I fixed 3 TODO comments warnings and there is one new warning because there is a new version available for one of the nf-core module that we are using. nf-core lint

╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔] 159 Tests Passed  │
│ [?]  37 Tests Ignored │
│ [!]  39 Test Warnings │
│ [✗]   0 Tests Failed  │
╰───────────────────────╯

I run the pipeline locally in stub mode. It completed successfully in all these cases:

nextflow run main.nf -stub -profile test
nextflow run main.nf -stub -profile test,docker 
nextflow -log "foo.log"  run main.nf  -stub-run -profile test,docker
nextflow -log "foo bar.log"  run main.nf  -stub-run -profile test,docker

I verified that the nextflow log file was correctly copied to ./results/pipeline_info/nextflow.log in all cases.

Extra tests needed:

• Try with the -log option
• Run on juno with S3 url for the outdir
• investigate if there are unit testing options without introducing nf-test

PR checklist

• [x] This comment contains a description of changes (with reason).
• [ ] If you've fixed a bug or added code that should be tested, add tests!
• [x] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• [x] Make sure your code lints (nf-core lint).
• [ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• [ ] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• [x] Usage Documentation in docs/usage.md is updated.
• [ ] Output Documentation in docs/output.md is updated.
• [ ] CHANGELOG.md is updated.
• [x] README.md is updated (including new tool citations and authors/contributors).

[LysianeBouchard]

Closing pull request as it is already addressed through other PRs.