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3 - Write background list#245

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WackerO merged 2 commits intoqbic-pipelines:devfrom
WackerO:write_bg_list
Jul 22, 2024
Merged

3 - Write background list#245
WackerO merged 2 commits intoqbic-pipelines:devfrom
WackerO:write_bg_list

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@WackerO WackerO commented Jul 19, 2024 •
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Added background list to output for reproducibility, removed hard-coded gprofiler DBs from report.
Also slightly changed the report text that shows when the gprofiler GMT file could not be downloaded so that it integrates better into the surrounding text.
This PR directly raises the pipeline version to 2.4 instead of setting it to dev as I will release after this PR

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
  • 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 Jul 19, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 34af7c2

+| ✅ 172 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-22 10:34:47

@skrakau skrakau self-requested a review July 19, 2024 09:29
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skrakau commented Jul 19, 2024

Hi Oskar, could you generate separate commits and PRs for different topics? It greatly facilitates reviewing and maintenance, i.e. traceability of changes. For example, a separate PR for the version changes, and separate commits for the different changes in the report.

skrakau
skrakau reviewed Jul 19, 2024
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Comment thread CHANGELOG.md Outdated
@WackerO WackerO changed the title Write background list 3 - Write background list Jul 19, 2024
skrakau
skrakau approved these changes Jul 22, 2024
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LGTM! :)

@WackerO WackerO merged commit df4c728 into qbic-pipelines:dev Jul 22, 2024
@WackerO WackerO deleted the write_bg_list branch July 22, 2024 11:28
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