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ampliseq samplesheet #361

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@brovolia
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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/fetchngs 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).

@github-actions
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @brovolia,

It looks like this pull-request is has been made against the nf-core/fetchngs master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/fetchngs dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@github-actions
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github-actions bot commented Oct 29, 2025 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 8d3a1cc

+| ✅ 182 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-fetchngs_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-fetchngs_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-fetchngs_logo_dark.png
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-10-29 12:42:25

@brovolia brovolia changed the base branch from master to dev October 29, 2025 13:52
@brovolia brovolia requested a review from drpatelh October 29, 2025 13:53
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@drpatelh drpatelh Awaiting requested review from drpatelh

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@brovolia @drpatelh @jenmuell