Add ms2rescore module, remove ms2pip and deeplc modules

jonasscheid commented 12 months ago

Addressing #288

Adding MS2Rescore and deprecating MS2PIP and DeepLC modules, since they are incorporated in MS2Rescore
Adding a couple of TODOs for an upcoming refactoring
Removed test_full from gh actions since this should be only used on the release PR. In the next refactoring iteration, a smaller sized quantification test will be implemented to cover the quant subworkflow
Some correction on citations and further documentation

PR checklist

[x] This comment contains a description of changes (with reason).
[x] 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] If necessary, also make a PR on the nf-core/mhcquant branch on the nf-core/test-datasets repository.
[x] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[x] Usage Documentation in docs/usage.md is updated.
[x] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[x] README.md is updated (including new tool citations and authors/contributors).

github-actions[bot] commented 12 months ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit e9a7527

+| ✅ 158 tests passed       |+
!| ❗   5 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `WorkflowMhcquant.groovy`: _Optionally add in-text citation tools to this list._ * [system_exit](https://nf-co.re/tools-docs/lint_tests/system_exit.html) - `System.exit` in WorkflowMain.groovy: _System.exit(1)_ [line 51] * [system_exit](https://nf-co.re/tools-docs/lint_tests/system_exit.html) - `System.exit` in WorkflowMhcquant.groovy: _System.exit(1)_ [line 18] * [system_exit](https://nf-co.re/tools-docs/lint_tests/system_exit.html) - `System.exit` in WorkflowMhcquant.groovy: _System.exit(1)_ [line 45] * [system_exit](https://nf-co.re/tools-docs/lint_tests/system_exit.html) - `System.exit` in WorkflowMhcquant.groovy: _System.exit(1)_ [line 51] ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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jonasscheid commented 11 months ago

There is an issue with adding extra features via psmfeatureextractor: If ms2rescore removes peptides for some reason (e.g. ms2pip does not support selenocysteine (U)), then the features of ms2pip are not present in the peptideHit. Unfortunately, psmfeatureextractor removes features that are not present in ALL peptideHits, meaning all ms2pip features are not added as extra features. We need to change psm_utils such that when updating peptideHits with rescoring features we make sure we remove every peptideHit that is not present in the psm_list of ms2rescore. Or we apply a filter within the ms2rescore_cli script

steffenlem commented 11 months ago

My test run should be finished tomorrow

nf-core / mhcquant