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New structure of mhc binding subworkflow #210

Merged
merged 21 commits into from
Sep 19, 2023
Merged

New structure of mhc binding subworkflow #210

merged 21 commits into from
Sep 19, 2023

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alina-bauer
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@alina-bauer alina-bauer commented Aug 29, 2023 •
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Update general structure of MHCbinding subworkflow according to this flowchart.
This is just the bare minimum structure without the prediction functionality.

  • We started with the mhc binding subworflow only for the peptide input type and only for the single input type (implementation for all kinds of inputs will follow)
  • The nf core modules for the new subworkflow were added, the functionality will be implemented in the py files corresponding to the modules or in the modules itself
  • The mhc binding subworkflow as separate workflows
  • The pipeline runs through without functionality --with-stub
  • The threshold handling will happen in the prepare_prediction_input step

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/epitopeprediction 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).

alina-bauer and others added 13 commits August 17, 2023 16:19
Restructure input check and samplesheet check
54ea01e
Add MIT license for check_samplesheet.py
9e1513b
Add information to CHANGELOG.md and fix bug in check_samplesheet for …
4110373 
…variant input
Black formatting
b974bd3
@alina-bauer
Update CHANGELOG.md
c74333b
@alina-bauer @jonasscheid
Add suggestions from PR to code
a645848 
Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>
Fix output printing and keep name inputtype for nomenclature of meta
4ec0102
Remove test code
01d1fea
@alina-bauer
Fixing valid sample sheet printing
776668e
@alina-bauer
Change nomenclature of file_type
e1eeebd
Black formatting
18507f6
@jonasscheid
Merge pull request nf-core#209 from alina-bauer/mhc-binding-subworkflow
50812f9 
Check sample sheet uses Row Checker class
Change nomenclature in samplesheet to inputtype that pipeline runs th…
62fac83 
…rough
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github-actions bot commented Aug 29, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 3839013

+| ✅ 159 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-09-19 11:26:48

Update general mhc binding subworkflow structure, bare bone implement…
03942bb 
…ation of mhc binding for peptides without functionality, runs through with stub
@alina-bauer alina-bauer changed the base branch from dev to mhc-binding-subworkflow August 30, 2023 09:24
@alina-bauer alina-bauer changed the title Change nomenclature in samplesheet to inputtype New structure of mhc binding subworkflow Aug 30, 2023
jonasscheid
jonasscheid requested changes Aug 31, 2023
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jonasscheid
jonasscheid requested changes Sep 19, 2023
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I'll take care of netmhc stuff, but looks good, after fixing small suggestions

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jonasscheid
jonasscheid approved these changes Sep 19, 2023
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if tests run through locally with stub LGTM

@jonasscheid jonasscheid merged commit a32a890 into nf-core:mhc-binding-subworkflow Sep 19, 2023
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@alina-bauer @jonasscheid