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Refactor for release 2.6 #310

Merged
merged 20 commits into from
Feb 27, 2024
Merged

Refactor for release 2.6 #310

merged 20 commits into from
Feb 27, 2024

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jonasscheid
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@jonasscheid jonasscheid commented Feb 23, 2024 •
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This PR comprises major restructuring to exploit the nextflow groupKey functionality. This change streamlines group-wise processing. Previously, nextflow waited until all processes of a module are done. Now, a downstream process is started once all files of a group have been processed upstream.

group_count and spectra (a key-pair that parses the spectrum filename) are now in the meta map to account for ordered grouping and splitting, especially in the quantification subworkflow.
Re-evaluating the quant performance of a spike-in dataset showed that the quantification performance is equally good.

Pre PR This PR
Pre PR This PR

Furthermore, 7 local modules were replaced by with nf-core modules. More to come 🚀. See #296

Lets merge this one before the template merge #307 to circumvent some additional merge conflicts.

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
temporarily disable neoepitopeprediction due to outdated vcf parsing
ffbb623
@jonasscheid
remove not needed ifEmpty(null) from versions channel
4dca345
@jonasscheid
use nf-core decoydatabase, remove local
3c8ff6b
@jonasscheid
remove not used fdr module
85c61ce
@jonasscheid
use nf-core peakpickerhires, remove local
f0629fe
@jonasscheid
add nfcore idmerger module, remove local
ccca493
@jonasscheid
update module patj
460c8c0
@jonasscheid
Use nf-core idfilter module, remove local
2136617
@jonasscheid
delete custom idfilter script
3af6c1b
@jonasscheid
delete pyopenms idfilter module
d4972ca
@jonasscheid
replace pyopenms idfilter with nf-core openms module
27c696f
@jonasscheid
add idscoreswitcher nf-core module
8f1a411
@jonasscheid
add nf-core module idripper, remove local
e37e9d6
@jonasscheid
introduce spectra meta key for easier merge and splitting, adjust qua…
2719b61 
…nt subworkflow accordingly
@jonasscheid
replace local with nf-core modules and adjust downstream channel hand…
7138ff9 
…ling
@jonasscheid
switch thermorawfileparser from local to nf-core module
49a5bb6
@jonasscheid
move thermorawfileparser config to nf-core section
5e54eb6
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github-actions bot commented Feb 23, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit e7a1938

+| ✅ 191 tests passed       |+
!| ❗   5 tests had warnings |!
-| ❌   8 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowMhcquant.groovy
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowMhcquant.groovy: Optionally add in-text citation tools to this list.
  • 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]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 53]

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-26 16:29:45

FriederikeHanssen
FriederikeHanssen reviewed Feb 23, 2024
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subworkflows/local/map_alignment.nf Outdated Show resolved Hide resolved
subworkflows/local/quant.nf Show resolved Hide resolved
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@jonasscheid @FriederikeHanssen
remove channel view
200865a 
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
marissaDubbelaar
marissaDubbelaar reviewed Feb 26, 2024
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I have a few suggestions, also related to the modules (although these are less important for this PR)

modules/nf-core/openms/decoydatabase/meta.yml Show resolved Hide resolved
modules/nf-core/openms/idfilter/main.nf Show resolved Hide resolved
modules/nf-core/openms/peakpickerhires/main.nf Show resolved Hide resolved
subworkflows/local/input_check.nf Show resolved Hide resolved
subworkflows/local/refine_fdr.nf Show resolved Hide resolved
workflows/mhcquant.nf Show resolved Hide resolved
marissaDubbelaar
marissaDubbelaar approved these changes Feb 27, 2024
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LGTM

@jonasscheid jonasscheid merged commit ce6ed23 into nf-core:dev Feb 27, 2024
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@jonasscheid jonasscheid mentioned this pull request May 30, 2024
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@marissaDubbelaar marissaDubbelaar marissaDubbelaar approved these changes

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@jonasscheid @FriederikeHanssen @marissaDubbelaar