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Fix mkfastq #253

Merged
merged 2 commits into from
Aug 19, 2024
Merged

Fix mkfastq #253

merged 2 commits into from
Aug 19, 2024

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nschcolnicov
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@nschcolnicov nschcolnicov commented Aug 15, 2024 •
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Addressing:
nf-core/modules#6189
#252

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 nschcolnicov requested a review from a team as a code owner August 15, 2024 21:00
@nschcolnicov nschcolnicov requested review from Aratz, apeltzer, grst and atrigila and removed request for a team August 15, 2024 21:00
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github-actions bot commented Aug 15, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 452e918

+| ✅ 191 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • 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 2.14.1
  • Run at 2024-08-15 21:02:05

@nschcolnicov
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The error I'm getting in the test is:
image

Which makes no sense, when I run it by myself it works just fine:
image

Will keep looking into this

@atrigila
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Looks like the first shard worked correctly with the mkfastq tests but the others are "empty" because there are no more tests to run. I would expect them not to run or to end successfully. Perhaps it is worth asking in nf-test.

@nschcolnicov nschcolnicov mentioned this pull request Aug 16, 2024
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@adamrtalbot
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@edmundmiller not familiar with the new sharding system, can you take a look?

@edmundmiller
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I haven't seen this either. Probably just merge and follow up on the nf-test issue is my vote.

@apeltzer apeltzer merged commit da9d837 into nf-core:dev Aug 19, 2024
4 of 9 checks passed
@apeltzer
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Merged it, can you please open an issue with nf-test @nschcolnicov / @atrigila 👍🏻

@nschcolnicov
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@apeltzer askimed/nf-test#245, done!

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@apeltzer apeltzer apeltzer approved these changes

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

@grst grst Awaiting requested review from grst

@atrigila atrigila Awaiting requested review from atrigila

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@nschcolnicov @atrigila @adamrtalbot @edmundmiller @apeltzer