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Rearrange quant and prepare for release 2.5.0 #280

Merged
merged 61 commits into from
Oct 3, 2023
Merged

Rearrange quant and prepare for release 2.5.0 #280

merged 61 commits into from
Oct 3, 2023

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jonasscheid
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Changes:

  • Depricated OpenMS RT prediction
  • Restructured quant to remove second FDR assessment and benefit from rescoring
    -> Merged percolator files are now split again into runs, filtered, aligned, quantified.
    -> With this we quantify the same peptide we obtain during Identification (core)
    Before:
    mhcquant_subway
    After:
Screenshot 2023-09-20 at 22 30 37

PR checklist

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

@jonasscheid
refactor naming
a58c7ed
@jonasscheid
more naming changes
da5ab1f
@jonasscheid
more namings
5f13484
@jonasscheid
Restructure quant part 1
5784677
@jonasscheid
Add post-alignment merger for featurefinder
71cf0f9
@jonasscheid
adjust such that quant_fdr can be used
ce8b6b7
@jonasscheid
restructure quant such that map alignment comes after percolator
cb0dca8
@jonasscheid
Update to openms 3.0.0
a9cfc37
@jonasscheid
replace dev container with mulled container on quay
4021716
@jonasscheid
Depricate old rt prediction
c26ddf4
@jonasscheid
depricate openms rt prediction
9488a4b
@jonasscheid
depricate openms rt prediction
d43c040
@jonasscheid
remove fastq image in docs
b0ff42b
@jonasscheid
adjust ffid settings
791258d
@jonasscheid
Update publishing files
ab0e4fd
@jonasscheid
Add scoreswitcher for quant and optional filefilter
8e5ae21
@jonasscheid
cosmetics
35c1919
@jonasscheid
Adjust publihsed files
2967a5b
@jonasscheid
filefilter optional in schema
8c9c92d
@jonasscheid
updated docs
c3e01cb
@jonasscheid
bump version
c600bf4
@jonasscheid
bump openms conda version
386788b
@jonasscheid
linting
c0d83a6
@jonasscheid
merge dev into feature branch, fix conflict
46835a9
@jonasscheid
update changelog
4ceb045
@jonasscheid
remove fastqc
e48f525
@jonasscheid
fix typo
0b43c85
@jonasscheid
update citations
2e81e78
@jonasscheid
fix lint
565d0fd
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github-actions bot commented Sep 20, 2023 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d59d2e5

+| ✅ 156 tests passed       |+
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.5.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMhcquant.groovy: Optionally add in-text citation tools to this list.
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 51]
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 18]
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 45]
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 51]

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-03 21:31:22

@jonasscheid
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jonasscheid commented Sep 28, 2023 •
edited
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Sorry that the PR is so huge.. the metadata was not properly processed through the rarely used subworkflows predict_class1 and predict_class2, therefore I needed to adjust these as well.

I added test, still need to wait for publicly availabe bruker data to add those tests.

Will need to merge the template update as well I guess..

@jonasscheid
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Template merged ✅

marissaDubbelaar
marissaDubbelaar approved these changes Oct 3, 2023
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Minor comments, LGTM

CHANGELOG.md Outdated Show resolved Hide resolved
bin/get_ion_annotations.py Show resolved Hide resolved
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@jonasscheid jonasscheid merged commit 87141eb into nf-core:dev Oct 3, 2023
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@marissaDubbelaar marissaDubbelaar marissaDubbelaar approved these changes

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