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Merged
itrujnara merged 13 commits into from
Oct 14, 2024
Merged

Merge template version 3.0.1 #61

itrujnara merged 13 commits into from
Oct 14, 2024

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@itrujnara
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@itrujnara itrujnara commented Oct 10, 2024 •
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Merge template 3.0.1

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

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github-actions bot commented Oct 10, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f102a12

+| ✅ 229 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  10 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.1
  • Run at 2024-10-10 09:12:02

maxulysse
maxulysse reviewed Oct 10, 2024
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conf/test_fasta.config Outdated
Comment on lines 17 to 18
memory: '6.GB',
time: '6.h'
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@maxulysse maxulysse Oct 10, 2024

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why not 15.GB and 1.h as you now have in the default tests?

maxulysse
maxulysse reviewed Oct 10, 2024
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maxulysse
maxulysse reviewed Oct 10, 2024
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modules.json
"git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
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@maxulysse maxulysse Oct 10, 2024

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you're missing the utils_nfschema_plugin

maxulysse
maxulysse reviewed Oct 10, 2024
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minor comments, should be easy to fix

@itrujnara itrujnara requested a review from maxulysse October 10, 2024 09:11
@itrujnara itrujnara merged commit 98a77b6 into nf-core:dev Oct 14, 2024
@itrujnara itrujnara deleted the merge-template-3-0-1 branch October 14, 2024 08:06
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@maxulysse maxulysse maxulysse approved these changes

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@itrujnara @maxulysse @nf-core-bot