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Overview figure update #94

Merged
merged 7 commits into from
Sep 13, 2023
Merged

Overview figure update #94

merged 7 commits into from
Sep 13, 2023

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tillenglert
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@tillenglert tillenglert commented Aug 11, 2023 •
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I updated the workflow overview figure! If you're missing something or I should redo something please let me know @skrakau!

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/metapep 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).

@tillenglert tillenglert marked this pull request as ready for review August 11, 2023 04:37
@tillenglert tillenglert requested a review from skrakau August 11, 2023 04:37
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github-actions bot commented Aug 11, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit dbc777a

+| ✅ 155 tests passed       |+
!| ❗  11 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-09-13 09:18:47

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skrakau commented Sep 7, 2023 •
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A few thoughts:

  • "Split into prediction chunks" I would omit, since this is more an implementation detail
  • the flow of the figure is a bit Zickzack :) I would aim at a straight path for the main part of the workflow, since this would be easier to grasp on the first view
  • MultiQC is not that important here, while I would put more focus on the visualizations. Maybe one could change "Downstream analyses" to "Downstream analyses and visualizations", and remove the MultiQC here
  • the peptide predictions and data model tables are not a result of the last "Downstream" block, thus the MultiQC report, Peptide predictions and Data Model Tables files could be moved if it helps
  • "Report stats": maybe omit the details. this could be also listed at the end of the workflow (if it helps) next to the other output, that it is generated already before is probably not important here
  • maybe if the path would be less Zickzack the, the show supported models would also appear more as an alternative running option

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skrakau commented Sep 11, 2023

That's already much easier to read. I have a few more notes, but feel free to do it differently:

  • "Peptide predictions" -> "Epitope predictions"
  • "General stats of ..." I would keep the short form from before "General stats"
  • "--show_supported_models": I would discard this parameter, the users can figure out themselves how to run this part
  • "Aternative path": there is one box more than for the other part, maybe move the text into the inner box and remove the outer box? Maybe one could even omit the inner green box (since it's not an extra tool and it's not default) and just use the title "Show supported models (alternative path)" (as you did for "Generate peptides")?
  • "Pipeline results": I think you could omit the outer box here as well and move the title to the inner box
  • "Downstream plots": nitpicking, just "plots" or "visualisations"?

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skrakau approved these changes Sep 13, 2023
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Looks great! :)

@tillenglert tillenglert merged commit abbbfa2 into nf-core:dev Sep 13, 2023
@tillenglert tillenglert deleted the overview_figure_update branch September 13, 2023 12:48
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