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patch bedtools/genomecov to use quay.io to solve issue with nf-core download #1393

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Merged
maxulysse merged 3 commits into from
Sep 30, 2024
Merged

patch bedtools/genomecov to use quay.io to solve issue with nf-core download #1393

maxulysse merged 3 commits into from
Sep 30, 2024

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@maxulysse maxulysse commented Sep 30, 2024 •
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  • Use quay.io for bedtools/genomecov to solve issue with nf-core download

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/rnaseq 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).

@maxulysse maxulysse changed the title patch bedtools/genomecov to use quay.io to solve issue with nf-core d… patch bedtools/genomecov to use quay.io to solve issue with nf-core download Sep 30, 2024
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github-actions bot commented Sep 30, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 894a770

+| ✅ 174 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-30 12:55:00

adamrtalbot
adamrtalbot approved these changes Sep 30, 2024
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Update the PR description!

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maxulysse commented Sep 30, 2024

Update the PR description!

title is enough

@maxulysse maxulysse merged commit fcbfa1b into nf-core:dev Sep 30, 2024
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