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Update samshee #275

Merged
merged 12 commits into from
Oct 22, 2024
Merged

Update samshee #275

merged 12 commits into from
Oct 22, 2024

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nschcolnicov
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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/demultiplex 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@nschcolnicov
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Created this PR for testing the module, I will update it after the nf-core module has been merged into nf-core/modules

maxulysse
maxulysse reviewed Oct 15, 2024
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conf/modules.config Outdated
Comment on lines 237 to 239
ext.json_schema_validator = { params.json_schema_validator ? "--schema '${params.json_schema_validator}'" : "" }
ext.name_schema_validator = { params.name_schema_validator ? "--schema '${params.name_schema_validator}'" : "" }
ext.v1 = { params.v1_schema ? "--output-format sectioned" : "" }
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I think we can put all that in a ext.args and not ressort to creating non standard ext

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@nschcolnicov nschcolnicov Oct 15, 2024 •
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Yes, I agree, this is still a draft

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Sorry for checking in on a draft, just working on a PR on this repo too, and I saw this one appeared and was curious

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Haha no worries! 😄 .Don't want you to waste your time reviewing something that might change regardless, but any help is always appreciated!

@nschcolnicov nschcolnicov marked this pull request as ready for review October 16, 2024 20:03
@nschcolnicov nschcolnicov requested a review from a team as a code owner October 16, 2024 20:03
@nschcolnicov nschcolnicov requested review from Aratz and removed request for a team October 16, 2024 20:03
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github-actions bot commented Oct 21, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a12681f

+| ✅ 202 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   8 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
  • schema_description - Ungrouped param in schema: strandedness

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-21 16:56:39

grst
grst approved these changes Oct 22, 2024
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The only downside currently seems that it's not possible to specify multiple samplesheets of any of the json/name/file types.

However, I'm not sure if anyone will ever use that and there are workarounds... So let's not overengineer that for now.

@nschcolnicov nschcolnicov merged commit 4d28759 into nf-core:dev Oct 22, 2024
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@grst grst mentioned this pull request Oct 24, 2024
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@atrigila atrigila mentioned this pull request Nov 5, 2024
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@maxulysse maxulysse maxulysse left review comments

@grst grst grst approved these changes

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

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@nschcolnicov @maxulysse @grst