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Changes for release2.3.0#399

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skrakau merged 5 commits intonf-core:devfrom
skrakau:changes_for_release2.3.0
Mar 2, 2023
Merged

Changes for release2.3.0#399
skrakau merged 5 commits intonf-core:devfrom
skrakau:changes_for_release2.3.0

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@skrakau skrakau commented Mar 1, 2023

  • updated Pandas version from 1.1.5 to 1.4.3 for processes depending only on Pandas
  • Removed the BUSCO_PLOT process. The new BUSCO version 5.4.3 would have required additional renaming of the short_summary files, since they are called "short_summary.domain.*" or "short_summary.specific_lineage.*" within this pipeline (see here).
    However, for the results when run with auto lineage selection, the current processing was inaccurate. One would need to select somehow, if the "short_summary.domain.*" or "short_summary.specific_lineage.*" file is used for this plot, while not both are present for all bins and using the most specific summary might not be best for comparison. Since anyway these plots are probably not designed for metagenomic bin comparisons, we decided to drop this process.

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/mag 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 Mar 1, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fa9fc7d

+| ✅ 155 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '2.3.0'
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-03-01 15:32:06

@skrakau skrakau requested a review from jfy133 March 1, 2023 15:18
d4straub
d4straub reviewed Mar 1, 2023
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d4straub
d4straub reviewed Mar 1, 2023
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@jfy133
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jfy133 commented Mar 1, 2023

For reference: furthermore the plot output wasn't doucmented so it wasn't 'officially' supported in a way :)

jfy133
jfy133 approved these changes Mar 1, 2023
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@jfy133 jfy133 mentioned this pull request Mar 1, 2023
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skrakau and others added 2 commits March 1, 2023 16:29
@skrakau skrakau merged commit 9b8cb40 into nf-core:dev Mar 2, 2023
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@jfy133 jfy133 jfy133 approved these changes

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