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Important! Template update for nf-core/tools v3.0.2 #276

Merged
merged 38 commits into from
Oct 17, 2024
Merged

Important! Template update for nf-core/tools v3.0.2 #276

merged 38 commits into from
Oct 17, 2024

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Version 3.0.2 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.0.2 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.0.2 release page.

@nf-core-bot nf-core-bot requested a review from a team as a code owner October 11, 2024 12:33
@nf-core-bot nf-core-bot requested review from glichtenstein and removed request for a team October 11, 2024 12:33
@nf-core-bot nf-core-bot mentioned this pull request Oct 11, 2024
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github-actions bot commented Oct 14, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0408378

+| ✅ 202 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.5.2
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-17 08:51:51

maxulysse
maxulysse reviewed Oct 14, 2024
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maxulysse
maxulysse reviewed Oct 14, 2024
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apeltzer
apeltzer reviewed Oct 15, 2024
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apeltzer approved these changes Oct 15, 2024
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Looks good to me - thanks for updating all the tests <3

apeltzer
apeltzer reviewed Oct 15, 2024
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maxulysse commented Oct 15, 2024 •
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Issues to solve:

  • Bases2Fastq: cannot get it to work, need to investigate the workflow
  • BCL-CONVERT-mini: Issues with a join, a null is used for meta.lane, but tries to join with a [] which fails.
    • When the null in meta lane is replaced by a [] other test fails, so need to investigate further how it's populated and fix all that.
    • Could be due to switching from nf-validation to nf-schema
  • FQTK: cannot get it to work, probably same issue as Bases2Fastq

@atrigila atrigila mentioned this pull request Oct 16, 2024
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@maxulysse maxulysse merged commit 61f48d6 into dev Oct 17, 2024
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@atrigila atrigila mentioned this pull request Nov 5, 2024
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@maxulysse maxulysse maxulysse left review comments

@apeltzer apeltzer apeltzer approved these changes

@glichtenstein glichtenstein Awaiting requested review from glichtenstein glichtenstein is a code owner automatically assigned from nf-core/demultiplex

@nh13 nh13 Awaiting requested review from nh13 nh13 is a code owner

@sam-white04 sam-white04 Awaiting requested review from sam-white04 sam-white04 is a code owner

@blajoie blajoie Awaiting requested review from blajoie blajoie is a code owner

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