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updating README + show_supported_models fix #225

Merged
merged 3 commits into from
Feb 16, 2024
Merged

updating README + show_supported_models fix #225

merged 3 commits into from
Feb 16, 2024

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thomas-davis
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Fix for #224

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).

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github-actions bot commented Jan 18, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8e4c198

+| ✅ 178 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.3.0
  • pipeline_todos - TODO string in WorkflowEpitopeprediction.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-epitopeprediction_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-16 08:04:02

@thomas-davis
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Minor pt. Looks like https://github.com/nf-core/epitopeprediction/blob/master/bin/check_requested_models.py still refers to FRED2 (old name of Epytope?) in a couple of places, I can roll that fix into this PR as well

@christopher-mohr
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Minor pt. Looks like https://github.com/nf-core/epitopeprediction/blob/master/bin/check_requested_models.py still refers to FRED2 (old name of Epytope?) in a couple of places, I can roll that fix into this PR as well

In which lines exactly? But in general, sure go ahead. :)

christopher-mohr
christopher-mohr approved these changes Jan 18, 2024
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Thank you! LGTM, just one comment

README.md
@@ -16,6 +16,17 @@
**nf-core/epitopeprediction** is a bioinformatics best-practice analysis pipeline for epitope prediction and annotation.
The pipeline performs epitope predictions for a given set of variants or peptides directly using state of the art prediction tools. Additionally, resulting prediction results can be annotated with metadata.

Supported prediction tools:

- `syfpeithi`
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we could also add references here (publication, website,...)

@christopher-mohr
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@nf-core-bot fix linting

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@christopher-mohr
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@nf-core-bot fix linting

@christopher-mohr christopher-mohr merged commit b6d9cf4 into dev Feb 16, 2024
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@thomas-davis @christopher-mohr