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Fix naming collisions#513

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JoseEspinosa merged 6 commits into
nf-core:devfrom
Kevin-Brockers:fix_naming_collisions
May 15, 2026
Merged

Fix naming collisions#513
JoseEspinosa merged 6 commits into
nf-core:devfrom
Kevin-Brockers:fix_naming_collisions

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@Kevin-Brockers

@Kevin-Brockers Kevin-Brockers commented May 2, 2026

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PR checklist

close #440
close #467
close #510

Fixes the issues above - I hope this is sufficient.
The suggested solution for: Performing one IP vs multiple different controls is to encode those comparison as multiple samples in the sample sheet, however this would trigger many unnecessary preprocessing (fastq qcs and alignments) of the same IP samples. Ideally we would avoid that.

However, I am not sure how often those situations will occur.

  • If you've fixed a bug or added code that should be tested, add tests!
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions Bot commented May 2, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0436058

+| ✅ 267 tests passed       |+
#| ❔   2 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   7 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 nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • 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 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

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-05-06 21:45:55

@Kevin-Brockers Kevin-Brockers marked this pull request as ready for review May 6, 2026 21:43
JoseEspinosa
JoseEspinosa approved these changes May 15, 2026
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@JoseEspinosa JoseEspinosa left a comment

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LGTM 🎸 Thanks @Kevin-Brockers!

@JoseEspinosa JoseEspinosa merged commit b6c5a4f into nf-core:dev May 15, 2026
6 checks passed
@Kevin-Brockers Kevin-Brockers deleted the fix_naming_collisions branch May 27, 2026 08:30
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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